These changes are always immediately updated in the "molden5.x.tar.Z" source file, however the platform dependent executables in the directory "/pub/molgraph/molden/bin" on the ftp site are not always in tune with the latest changes, check the date on the executable. ------------------------------------------------------------------------ Molden5.0.6 Tue Apr 9 - The functionality of adding hydrogens to hetatm residues was broken due to change in the web service pdbechem. With this version it is again functional. - gmolden: shader bug when using occlusion and Blur caused the screeen to not be updated correctly on some systems. - gmolden: Added a proper "balls & sticks" mode, next to the already existing sticks mode (in gmolden incorrectly named as balls & sticks). Molden5.0.5 Thu Dec 20 - Added to possibility to localize orbitals (boys scheme). Next to the 'orbitals' button there is now a 'local' button. Molden5.0.4 Mon Nov 26 - Added a ramachandran plot for proteins. It can be found as last option under the 'Surface' icon. - Fixed a bug that made the Average CH3 button disappear in the NMR spectrum. Fri Nov 9 - Restructured file selection so that it can now be generally used. Used the file selector in the "Read Grid" button in the density mode and also on the "Vr" button where you can map an other grid onto the first grid. Added a filter to the file selector, nothing fancy just a substring match. - Cleaned to code of molsint.f. Now when calculating distributed multipoles Molden will report when mxsite is exceded. This usually only happens when NO overlap contributions are shifted to atomic sites. - Somebody reported problems on his self constructed gaussian style files. Fixed this. - Added a charges scaling option to ambfor (for example : ambfor -S 0.7) - Ambfor will now parse a file called 'param' with alternative parameters (If it exists of course). Thu Sep 20 - Molden now by default no longer searches for mpi executables at start up. On machines with terabytes of disks this can take very long. - Updated reading of Orca files, so that geometry+gradient single point runs should now also be supported. Thu Sep 13 - Molden can now also read Gamess-US inputfiles with cartesian coordinates - Adjusted the writing of ambfor .xyz files so that the file can still be read by molden if there is an undefined atom type. Fri Jul 13 - Molden used to read in the first point with orbitals for Gaussian09 This was because in the beginning of its release, the orbitals of the stationary point were not printed. Currently Gaussian09 does print the orbitals of the stationary point. Now Molden will display the orbitals of the stationary point. Fri Jun 15 - Molden now check then openGL vendor string to circumvent a bug in the graphic drivers of intel video cards. This caused a segment violation on _mesa_generate_mipmap Thu Jun 7 - the .jdx file written with the use of the keyword PLECTRUM now also contains information for use in combination with jspecview and jmol. Thu Apr 26 - included wrting of a .jdx file with the keyword PLECTRUM - keyword SPACE=value now is honoured when reading cube/grid files Thu Mar 15 - Made the generated web pages for spectra (keyword PLECTRUM) compatible with Internet explorer. Tue Feb 28 - Improved generation of the html page created with the use of the PLECTRUM keyword. (see below Tue Feb 14). The command used to convert the postscript file now is: gs -sDEVICE=jpeggray -g1000x500 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps The index.html file now also contains javascript code to view the active normal mode as a red line drawn on the spectrum. It also contains a table of available frequencies together with intensities, they can be clicked. Tue Feb 14 - The molden keyword PLECTRUM calculates a spectrum for files that have frequency and intensity information, in addition it converts the postscript file that contains the spectrum to a jpg file. For the conversion to work the ghostscript program must be installed and defined. The folowing command is used to generate spec.jpg: gs -sDEVICE=jpeg -r500x250 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps It also creates the files index.html, mol.xyz and freq???.xyz. The last files contain animations of the normal modes. These can be used for interactive spectra in combination with the jmol viewer. - Rudimentary support for NWchem output files. Mon Feb 13 - The xyz format already supported dummys with the 'xx' element label. Now Banquo ('Bq') sites are also supported. Both are displayed with the 'xx' label. Fri Feb 02 - Added molden keywords SPECTRUM (and PLECTRUM) to calculate a spec.ps from a molden commandfile. Only for files that have spectra information. - Molden now visualizes a file with just one atom better. Fri Jan 20 - Added keywords EXTPOSCHG and EXTNEGCHG which specify a single pointcharge to be added for the calculating of the QM electrostatic potential. This can be used to model a counter charge when calculating the Elec. Pot. of an anion or cation. EXTPOSCHG=(r.rr,r.rr,r.rr) where r.rr is a real number representing the cartesian coordinates in Bohr. - Added commandline flag -U to switch of using shaders. On some graphics cards the opengl version (gmolden) can hang on setting up the shaders. Mon Jan 9 - Some optimisation to shader code for the benefit of older graphics cards under Ubuntu Natty Sat Dec 31 - The lines representation of a surface in Opengl shader language gave problems. Fixed it. Thu Dec 1 - Molden uses the pdbechem service to find out what hydrogens to add on ligands. Unfortunately, the URL for this service has changed. I have updated Molden to point to the new URL. Mon Nov 28 - Fixed blocky noise when using occlusion. Mon Oct 24 - amfor xyz files with cell information were not correctly stored in the internal common blocks of molden. As a result writing a just optimised structure and comparing it with the structure on screen would give different results. Fixed it ! Sun Oct 23 - Reading molden format files that contain only data for MO coefficients that are non-zero. When this file is not the first file read in it could occur that coefficinet that should be zero were actually non-zero. Fixed this. Fri Oct 21 - Fixed small bug that would leave a atom selected in solid mode hovering around when switched to line or stick mode. - gmolden using shaders would sometimes not draw a surface as transparent Mon Oct 17 - Added a bigger font for the labels of atoms and residues for the opengl version gmolden. Wed Oct 12 - added the commandline option '-k int' (int=0-15), to specify the color used to plot lables. Only available for the openGL version (gmolden). Thu Sep 29 - The by molden created *.ogl files can now also be read from the commandline: ./gmolden molden.ogl Previously, these files could only be read from the filemanager. Wed Sep 28 - fixed a bug that would leave the outvector of the plotplane essentially as a nul vector. This would only occur if you let molden figure out a default plane AND if the first three atoms would be on a line. Fri Sep 23 - Built in a button to make a gif screen shot in the density mode. - Pressing 'R' for shadows now does not make the background black when no shader capability is found. - when writing a ambfor .xyz file with crystal information, now also expands the cell before writing. Thu Sep 15 - GAFF atom type assignement: switched from default aromatic Nitrogen type nb to nc. (nb is only for pure aromatic compounds such as pyridine) - also truncated negative values (see Wed Sep 14). Wed Sep 14 - fixed problem with writing cube files on 64-bits platforms. Function values that are less than 1.0d-99, are 'truncated' to 1.0d-99 Mon Sep 5 - Fixed a bug in the C code that calls getpoi (Thanks to Ben Roberts, University of Florida for fixing this). This bug could affect the processing of Gaussian files. - When there is only one (hetatm) molecule in a PDB file, molden would not pass on the total charge to the routines that calculate partial charges, even when it offered the possibility to set it. Fixed. Thu Sep 1 - when the main window was resized (or -geom commandline option was used) in the opengl version (gmolden), the rubber selection band for selecting atoms in the z-matrix editor was wrongly displayed. This is now fixed. - when assingning charges to hetatm molecules of pdb files, molden would try to retrive the total the total charge from the pdbchem. If no valid three letter residue identifier was defined it would return charge option -15, as a result the default total charge in the "assign total charge" window would be "quintet" in stead of "0". Such a situation would accur when a ligand was added by combination of two structures in the structures window. Thu Aug 18 - When using xming as xwindows/opengl emulator, in the opengl mode when using the "select by pointer" mode in the z-matrix editor, the rubberband would not be drawn. This is now fixed. Tue Aug 16 - When writing a Gamess-US style z-matrix and when variables were specified as constants, Molden now writes an ifreez record and nzvar. Wed Aug 10 - Added visualisation of calculated UV-spectra from TD-DFT calculations with Gaussian. Please feel free to suggest improvements. Mon Aug 8 - Fixed a bug which could make molden crash when having multiple structures. - The output of the internally run 'locate' command on linux is now redirected to /dev/null. So unsuspecting users are not confused. - Added small tweaks to the gaff forcefield types assignment (nitrogen in cyanide is now typed). - Added a lot of ifdef statements to make sure older linux distributions do not include the newer code for OpenGL shaders. Mon Aug 1 - Fix for reading gaussian 09 output when coordinates were frozen. Wed Jul 13 - reading of esp charges on gaussian output has now been put before reading of basis-set. This way when no basis-set is written the esp charges will still be read. Mon Jul 4 - The 3D wireframe drawing (X-windows) of the density/orbital mesh was no longer drawn with equal width and height when using the commandline -geom 1600x800 qualifier (example). Fixed it. The use of shadowmaps currently only works if you dont resize. Thu Jun 30 - Introducing Shadow mapping, for proteins, the secondary structure cartoons cast shadows on them selves. See the palette icon, option shadows. Or just hit 'r' in the drawing screen. Tue Jun 7 - Introduced a bug in reading multi xyz formats, some month ago. Fixed it. Tue May 31 - There was a bug reading Mopac2009 output Mon May 16 - Molden now prevents the jobname being the same as the file being currently read. This can cause problems. Wed May 12,13 - Removed a bugs from the mpi MD code. Thu May 5 - gmolden will draw proteins faster in the space filling mode. Wed May 4 - gmolden would be killed due to too much memory consumption, during an MD run, fixed. - xyz files containing more than 1000 structures, are now all accounted for in the geom conv. window. Thu Apr 28 - There is a bug detected in the fast water code of ambmd. I have applied a temporary quick fix. Tue Apr 12 - Added postprocessing options: Blur and Occlusion to the colorpalette icon. These options work as toggles. It will slow this down a bit, certainly on less powerfull systems (graphics card dependant). This is only available if you run molden locally. - Changed the default for gmolden (mixed openGL/Xwindows executable) to be fullgl. You can still get the old mixed behaviour by using the commandline option -F. - Molden does now also better support the mol2 file dialect used by the popular docking program FlexX. - When calculating the contacts between a ligand and residues in opengl mode, the distance labels where not correctly displayed at far away distances. Fixed it. Wed Apr 6 - input z-matrices having variable names longer than 8 characters were not read in. I have now increased the maximum variable lenght to 10. Wed Mar 16 - Molden now has per pixel lighting built in. This looks a lot better, especially the specular lighting. The per pixel lighting is accomplished with shaders. Windows emulators like Xming and Xwin32 do not support shaders, so you will not see a difference there. Mon Mar 14 - Molden compiled with gfortran had problems with reading the protein density file, fixed it. - Molden compiled with gfortran sometimes crashed when reading in a second structure, fixed it. Wed Mar 2 - Added a cutoff scheme for water-water interaction, see: Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics Cristopher J. Fennell and J. Daniel Gezelter, Journal of Chemical Physics. 124, 234104 (2006) - Adapted the makefile to be a little more intelligent. It now tries to figure out on what os it is. This will cover most flavors of linux, MacOSX and cygwin. Fri Feb 25 - Added support for the Gaussian 09, new IRC mode HPC. By request of Prof. Ugo Cosentino Thu Feb 17 - added a routine for water-water interections. It uses a lookup table. It is unfortunately only a little bit faster (factor 0.66) Fri Feb 11 - removed a bug that would not copy all of the force field information after allocating memory for a water filled box. Thu Feb 3 - Adding ions is now done depending on the electrostatic potential. You can still invoke random placement with the commandline argument -z on ambfor/ambmd (in combination with -b). Wed Feb 2 - replaced use of fork by vfork in an attempt to stop forking errors on windows7 (64bits version still has problems). - When adding a water box in ambfor or ambmd automatically ions are added to neutralise the box. The placement of the ions is accomplished by replacing waters randomly Fri Jan 28 - there is now also a multiprocessor version of the crystal optimiser. - removed a small bug in the opengl version when reading a jaguar cube file. Tue Jan 25 - The molden/gmolden interface will now automatically detect whether the openmpi executables have been built. If so an option to use multiple processors will be availabe in the window that fires ambfor/ambmd jobs. - Removed a bug in the multiprocessor version of the MD program, ambmd. Each subprocess would have its own initial velocities, which in turn would lead to different coordinates in each subprocess. Fixed it. Thu Jan 13 - Finally got the interactive optimisation working flawless on WindowsXP. - Fixed continued rotation during interactive optimise. - optimised update time during optimisations Wed Jan 5 - Added atom type 'cz' to the GAFF force field, this is needed for guadinium and arginine. Also added improper torsion to keep the C connected to the three N's in one plane. Tue Dec 7 - Crystal optimiser was only working for non-covalently bound crystals. Current version has been tested on organic crystals and seems to work. Molden5 - Added a crystal optimizer, based on the gaff force field. Periodic conditions are enforced by translation symmetry copies. NO ewald summations ! This is a beta test. - Gamess-US irc data, bug fix. first atom was not displayed - While adding support for the calculated NMR spectra, a bug was introduced that made it impossible to set the maximum intensity in a spectrum. fixed. - When doing a combine structure on two proteins, the ligands are now also colored by structure. - When using combine + align on two none protein structures, the user is asked to specify 3 pairs of atoms. Each pair consisting of one atom from the first and one atom of the second molecule. The code has been changed in such a way that only atoms can be selected of the first/second structure. - Adapted molden to be more vista/windows7 friendly. - When aligning two structures no longer the pmf score window pops-up after pressing escape two or more times. - the interface to qchem and orca was only partly functional. Fixed it. - The crystal information of a mol2 file was nolonger parsed, fixed it. ------------------------------------------------------------------------ Molden4.9 Wed Sep 22 - Updated molden to read gaussian09 IRC caclulations outputs. Wed Aug 11 - Updated Updated reading of Gamess-us output, kindly supplied by Mariusz Klobukowski. The number of electrons when using pseudopotentials is also calculated correctly. Mon Jun 21 - Updated reading of Gamess-us output, kindly supplied by Mariusz Klobukowski 1) to read results from hessian calculation in the latest version of gamess-us (lines with mode symmetry information were added) 2) to read basis sets in semiempirical calculations (we changed gamess-us to be able to see the semiempirical MOs, with the STO basis sets expanded in terms of STO-nG expansions). Thu Jun 17 - The reading of a gridkont file (Program GRID) has been moved from the density mode to the molecular mode. Under the surface icon, there now is an option "gridkont". The benefit of this move is visualisation of the GRID molecular interaction together with the full opengl protein visualisation and the use of clipping planes. - added a box around the grid for gridkont and protein electron density. Wed Jun 2 - Added the option to for the electron density to follow the current residue. This build on a feature of molden to show the label of the residue the pointer is currently over. In addition now also a block of electron density follows the residue the pointer is currently over. You can fix the postion of the block, by hitting the spacebar. Hitting it again will make the block follow the pointer movement again. This all in the context of the latest hanges to molden of Fri May 28. See below. Fri May 28 - Under the surface icon, there was the option electron density map. Clicking this would try to read a file contaning protein electron in the so called 'omap' or DSN6 format. These files are available from the Electron Density Server at Uppsala University: http://eds.bmc.uu.se/eds/ This functionality has been extended. When reading a pdb file the pdbid is automatically parsed and stored. When clicking the "elec. Dens. Map' option the pdbid is used to automatically retrieve the omap file from the electron density server. (the program wget is used for this). After the file is read, a window will pop up, where you can specify the electron density contour level. The rendered electron density volume can also be clipped in three directions, for clarity. - on request from Paolo Tosco, molden4.9 now allows upto four keyword lines in a molden keyword file. Wed Apr 21 - When reading a protein ambfor .arc file, the secundury structure would be all coils, fixed this. Mon Apr 19 - When interactively omptimising a structure with a water box, molden sometimes would not show the waters. Also aborting the optimisation by pressing escape, would sometimes disrupt the X protocol. Fixed. - Updated the windows version. Wed Apr 14 - When a ambfor xyz file was loaded after a pdb file, its secundary would be all coils. Fixed. Tue Apr 13 - When reading a ambfor xyz file, nolonger the hydrogen bonds are calculated by default. In the presence of a big water box this becomes very slow. - Going into the zmatrix editor the waters were stored. After quitting the zmatrix editor, the waters were restored. However in the presence of a large water box, the restoration was very slow. Fixed. - Using the default optimiser(lbfgs) now also the waters that water out of the box are come in to the other side of the box. Mon Apr 12 - When interactively optimising a small molecule , in the presence of water box, the waters and box would not be visible in the line drawing mode (solid was ok). Fixed. The box itself is now also visible. - In the residue command window, when multiple chains were available, you would have to specify the chain also in order to visualise residues. This is now changed. You can however still use the chain identifier: *:A for example will switch on all residues belonging to the A chain. - When reading an ambfor xyz file containing a protein, and subsequently writing a PDB file, every first residue of a chain had residue number 1. This caused probelms when there were chains consisting of 1 residue. Such a pdb file would not parsew correctly. Now all residues have a unique number. - reading an ambfor xyz file with a box specified, would lead to an empty screen when opening the z-matrix editor. This is fixed. - When optimising the Hydrogen positions, waters that are close to a metal center now also have hydrogens added. - Water boxes containing more than 5000 waters would have a corrupt [RESIDUE] section in the ambfor xyz file. This would lead to artifact in visiulisation with molden. Wed Apr 7 - ambfor: made ff99sb the default protein force field. The unmodified amber 99 force field will be used when specifying the -x commandline flag - ambfor: for rna/dna modelling the ff99bsc0 modification of the amber force field will be used when specifying the -y commandline flag - fixed a bug that would visually screw up the secundary structure, when in the xwindow mode. - in the standard molden xwindow version the residue popup windows, would have options, when clicked would activate the wrong action. This bug was introduced the week before. Thu Apr 1 - absolute scores for histidines were still to big, relative scores were already OK. - fixed a bug is the secundary visualisation, which under very special circumstances would not show part of the coil. - The small amino acid menues you can bring up by clicking with the second mouse button now also contain an option to change the protonation states for histidine, and a flip option for asn and gln - In ambfor the total charge on non amino acid residues is checked and corrected if it does not add up to a discrete integer. Thu Mar 25 - fixed a major bug in calculating the scores for histidine (D,E,+), under the optimise hydrogen positions. - added prediction of asn/gln flips, under the optimise hydrogen positions Fri Mar 19 - Fixed a bug that could make the hetatm residues disappear in the z-matrix editor, when previously "Opt H pos." was used. - when aligning two protein structures, both structures have a different color. Also in the backbone mode the secondary structure visualisation will have a different color per structure. - when combining two small molecules from the structure window, you will now be asked to move the two structures into visible range. - when using command from the residue command window in combination with the SURF keyword, molden will now display opengl surfaces in opengl mode. - cysteines missing an HG atom will now have partial charges adding up to -1. This also implemented in ambfor. - some pdb structures containing hydrogens with labels not recognised by molden are now recognized. There are probably more, let me know if you find more. - fixed a bug that would make some surfaces not being displayed in the surfaces window. This could also cause: surface OFF, not to work. Mon Mar 8 - added ambfor support for modified nucleotides such as: 1MA,5MC,OMC,2MG,M2G,7MG,OMG,YG,H2U,5MU,PSU NOT supported are: 1MG,I,+U - water oxygen atoms connected to the protein are disconnected before writing ambfor xyz files. Wed Feb 24 - fixed a minor bug that would give a superposed atoms in z-matrix, after doing optimise hydrogen positions on a dna molecule. Tue Feb 23 - for rna to z-matrix molden now takes an OXT atom in to account. Mon Feb 22 - Added parameters for nucleotides to the amber force field implementation in molden and ambfor. - corrected charges for water, which did not completely add up to zero. Mon Feb 1 - G09 has different zmatrix output than G03. Molden can now deal with this. Tue Jan 26 - Molden4.9 introduces to optimisation method lbfgs as default optimisation algorithem for Ambfor. Together with some other code optimisations, this increases the speed of ambfor with a factor 4. - changed param.f, such that less continuation lines are used. The many continuation lines caused problems with compilers such as ifort. Wed Dec 23 - more bug fixes concerning interaction between Molden with Tinker and Ambfor. Tue Dec 22 - MAJOR Bug fixes concerning interaction between Molden with Tinker and Ambfor. For ambfor the bug was introduced on 27 November, when the writing of ambfor xyz files was changed. This bug is now fixed. Ambfor will now write a file 'ambfor.wr' to indicate it is writing intermediate optimisation files, when done writing it will remove this lock file. This improves the interaction with Molden, which in some cases would begin to read the file when its writing was not yet complete, resulting in incomplete structure on screen. The interface with Tinker was compromised earlier when ambfor started to write intermediate files in binary form. Tinker and Ambfor now have their own reading routines. The jobname.run file, a csh script now has a -f added to the #!/bin/csh line. This is because .cshrc files could contain commands preventing the succesful executing of this file. An number of buttons not applicable to Tinker jobs are now nolonger visible in the Tinker optimise window. Sat Dec 19 - fixed a small bug that interfered with wget, which molden uses to fetch pdb and hydrogen positions to add to ligands. - fixed a bug that would make ambfor crash when using the -N option in combination with a liagnd being present Thu Dec 17 - The switching function for the electrostatic used with cutoff with ambfor caused distortions of the final protein geometry. I switched to a shifting function for the electrostatics to solve this problem. - The use of switching/cutoffs (commandline flag -N) in ambfor/ambmd is now twice as fast. Mon Dec 14 - Open shell stuctures are now also read from a Mopac2007 .aux file. - Molden now tries to find the environment variable g09root - Fixed a small bug that could make Molden crash after reading in two large structures. - Fix that treats negative J-couplings correctly (NMR from gaussian) Thu Dec 10 - In addition to 1H NMR, molden now also calculates the 13C NMR spectrum. - The magnetic shielding and J-coupling corresponding with rotationally equivalent Hydrogens can be averaged by clicking the corresponding Button. Wed Dec 9 - Molden can now display caculated H NMR spectra from gaussian You need to have caculated magnetic shieldings and J-couplings Mon Nov 30 - Fixed bug in reading nmr data from gaussian output. Fri Nov 27 - Ambfor can now be run using cutoff's and switching functions: use the -N commandline flag to use cutoffs and switching. This can be faster than all atom optimisation ( a lot). The window form which ambfor optimisations can be fired from Molden now also has a button to use cutoff's and switching. - When writing ambfor files the order is now such that ambfor can work with contigous molecules. The ambfor file now contains an extra sections '[RESIDUES]' which contains the begin of amino acids and hetatm ligands (including water). - The ambfor and ambmd now catch the user's Control-C and now flush the buffer before exiting. - Ambfor now handles better finding equivalent parameters for covalently linked ligands to aminos acids. - Ambfor can now be run using cutoff's and switching functions: use the -N commandline flag to use cutoffs and switching. This can be faster than all atom optimisation ( a lot). Fri Nov 20 - When using Gaussian with the keyword NMR, the nuclear shieldings are read and can now be displayed as a label. If also J-couplings are available and extra "J" button will appear in the "calculate" section. When clicking it, select two atoms and the their J-coupling is displayed in the calculate window. Sun Nov 15 - Removed a bug that affected the prediction of HID/HIE histidine residues. Tue Nov 10 - Optimisation of Hydrogen positions under "H" icon, now also includes getting the formal charges of HETATM residues, adds hydrogens if not added already and calculates the partial charges of the hetatm residue. It then optimises the OH positions of THR, TYR, SER resiudes. Then it optimises the the choic between HIE and HID histidine residues. Finally it adds hydrogens to the water molecules , that are in close contact with the protein. - the atom attributes window now also offers an editable field for the atom number. Which makes it easier to identify an atom on screen, when only its atomnumber is known. Wed Nov 4 - The generation of charges on a pdb file is now more verbose. It also does nolonger consider the amino acids, since they have charges from the ambfor forcefield. For each HETATM residue, the charges are calculated separately. - Molden now also writes HETATM residue names, when writing a PDB file via the "write" button. - When charges are calculated for a HETATM residue, the VDW surface colored by electrostatic potential is now supported. Tue Nov 3 - The Hydrogens added to HETATM residues, are now put directly after the the residue. This way it does not interfere with other fucntionality such as interactive docking and interactive optimalisation. Sun Nov 1 - Removed bug parsing PDB entries like 1eat, which have more than two alternative residues - Made routines to add hydrogens to HETATM residues crash proove when no residue is recognized. Thu Oct 29 - added routines to add hydrogens to HETATM residues from the PDB. The default uses the web server from PDBeChem. It uses the external program 'wget' for this. If you dont have it, you can retrieve it from: http://ftp.gnu.org/gnu/wget/ A second fallback method adds hydrogens by looking at the angles of the atom it coonects to. This method is far from ideal or unambiguous - added the possibility to retrieve a PDB file from the internet. It uses the external program 'wget' to do this (see above). You will find a "Get PDB" button and text entry field in the file selector. - When element information is available from columns 77,78 in the HETATM record of the PDB file, this is now used to determine the element type. The old method, which uses the atom label to determine the element type, is still used for old style pdb files. Wed Oct 21 - Sometime back the MS-DOS fileformat check was introduced, for files supplied at the commandline (for files via the file select window this was already in place). However, when a non-existent file was specified, an empty file with that name was mistakenly created. This is now fixed. - In case that there are intensities together with frequencies, both are now listed together in the frequency list box. Tue Oct 20 - when reading a pdb structure from the commandline, followed by 2nd mouse button click on and hetatm residue -> "Mol. -> Structure" molden would crash. Fixed it. Mon Oct 19 - Added optimisation of water to the H optimise option. Waters acting as donors/acceptors to a residue, have hydrogens added. Other waters are deleted. - An error in reading AMBFOR .xyz files no longer leads to an exit from the program. - when reading an AMBFOR .xyz file, the error printing has now improved. - removed a bug in ambfor (which can reveal it self after new memory allocation. Mon Oct 12 - Changed the default for a histidine residue to be Neutral (HID). The option under the H icon, "Opt. Ser/Thr/Tyr/His H", will now also select which histidine is the best HID or HIE (both neutral). positive HIS has to be created via the z-matrix by adding a H to the neutral histidine. - In Opengl mode structures would not be updated after zmatrix editing of a protein, fixed. Fri Oct 9 - removed bug that would switch hetatms to visible when in backbone mode, after setting a distance monitor. - when switching from stick to solid in gmolden (opengl) already set distance monitors would no longer be visible. Fixed it. - Fixed a bug that sometimes would ambfor crash when allocating more memory - added the option the optimise the hydroxyl hydrogens positions of the threonine, serine and tyrosine residues. Under the H icon. Mon Oct 5 - removed bug which under certain conditions would not correctly show the opengl secondary structure of the second structure read in (gmolden). Fri Oct 2 - Some more fullgl opengl version of gmolden updates. - removed opengl helices/strands/coils during an optimisation, since they were not updated. Thu Oct 1 - The fullgl opengl version of gmolden (as opposed to the mixed xwindows/opengl version) has a few bugs fixed. In the lines mode, during an protein movie the residues would not be updated. Now they are. - The distance monitor now also works during a protein movie. Mon Sep 28 - when creating a water filled box with ambfor/ambmd, some of the waters at the edges could be very close to waters in neighbouring cells. When using this box in MD this would result is waters with very high velocities. This problem is fixed now. Thu Sep 24 - Gaussian09 MP2 energies are now correctly read. Fri Sep 18 - Fixed a problem introduced in molden4.8 with reading AMBFOR xyz files. specifically recognising protein structure. - fixed some of the things that dont work when running the full opengl version of gmolden (-F commandline) flag. There still remain some issues. - The zmatrix is NO LONGER updated during a movie - Scroll wheel now also work in interactive optimisation mode Thu Sep 17 - more updates to swooth the interaction between molden/gmolden and ambfor/ambmd - You can now add a water box to both force field and md simulation. - When ambfor xyz/arc files are read in, the element types are mapped from the integer atom type, and nolonger from the atom label Fri Sep 11 Molden4.8 - Molden4.8 introduces ambmd: Added a simple isotropic MD program to the ambfor program. The Molden interface can now fire these MD jobs via the optimise (AMBFOR) window. You can now select 'ambmd' in addition to ambfor. - the ambfor and ambmd programs now have a -b commandline flag, which will add a waterbox to your structure - ambmd produces a .arc file as the trajectory file. The reading of this file in molden has been speeded up. Wed Sep 2 - When adding the possibility of contraints to optimisation with ambfor, it was overlooked that in the event that no restraints were set, all atoms in the ambfor xyz file would be treated as fixed. This has now been corrected. - Water was not handled well in ambfor, fixed it. Thu Aug 27 - Added a simple isotropic MD program to the ambfor program. The Molden interface can now fire these MD jobs via the optimise (AMBFOR) window. You can now select 'ambmd' in addition to ambfor. Thu Aug 20 - When reading G09 output, molden now correctly deals with the fact that G09 only prints orbitals for the input geometry and nolonger prints orbitals of the stationary point. - Molden now also recognizes MSDOS files supplied via the commandline and automatically converts them to unix formatted files. Wed Aug 12 - reading back in ambfor generated xyz files, the amber atom types have automatically charges assigned Tue Aug 11 - further compatability fix for reading g09. Thu Jul 23 - fixed serious bug in reading gaussian output, while creating support for g09. Fixed ! - reading back in ambfor generated xyz files, the supported amber ions are now correctly classified by element. Tue Jul 21 - first support for gaussian 09 single point, simple optimise, simple force/freq jobs supported More updates are probable to follow Sun Jul 19 - Removed a number of bugs concerning reading the latest Gamess-UK output. Fri Jul 17 - Reading gamess-uk output with more than 99 points in the geometry optimisation, all point above 99 would not be updated, fixed it. - The energies from the latest Gamess-UK output are picked by molden and shown in the geom. conv. window. - The fullgl version of molden would not update the background color when changed with the paleete icon: fixed Wed Jul 15 - fixed recently introduced bug, reading 3dgridfile Mon Jul 13 - Partial optimisation can now run in BFGS optimisation mode in ambfor upto 330 flexible atoms. - Molden reads back in ambfor .xyz files better. - Updating labels no longer lags in slow connection opengl mode. - Resizing main screen in opengl is now one update. Tue Jul 7 - Added the possibility of partial optimisation. If you want to optimise a docked pose, select only the ligand and the surrounding residues flexible. And optimise with the the amber/gaff force field. - Molden now supports the scroll wheel to zoom in and out. - When using starnet X-Win32 X-windows server, gmolden switches to use full OpenGL (not mixed xwindows/opengl mode). The newer versions of X-Win32 ver 8, have problems with zooming in via the Ctrl key, in this case use the right Control key or the scroll wheel. - Molden can not determine which version of X-Win32 server is active. You can use the molden commandline flag -Q, to return to the mixed OpenGL/Xwindows mode. This will work better with older versions of X-Win32 (6.1 and older). - When aligning two small molecules and using the align and combine option, there was an extra copy of one of the molecules. Fixed it. Wed Jun 3 - Removed bug from the handling of the multi mol2 and sdf files Fri May 28 - Added the option to compile a complete GL version of gmolden. Uptill now gmolden did some graphics in xwindows and most graphics in OpenGL. In the MacOSX version of gmolden, the xwindows graphics were not visible. I therefore created the option to let gmolden do all graphics with OpenGL calls. You request this new functionality by adding the -F command line flag. Mon May 4 - fixed annoyance that during animations, the animation would stop because of the help window popup on the button started the animation. Tue Apr 28 - fixed bug that could screw up the displaying of secundary structure in the opengl version of molden, in the case of multiple proteins being loaded. Mon Apr 27 - Multi molecule files, such a .sdf files and .mol2 files will now open an extra window in which each separate molecule is clickable. - In addition you can now combine .mol2 files conataining poses for a ligand with the protein being docked into: First load protein. Second, read multi mol2 file with "Add" selected in the read file window. Wed Apr 16 - added the calculation of topological polar surface area (PSA). Molden control window -> surface icon -> totpol. PSA - added the calculation of the Quantum Mechanical PSA, fisrt calculate a 3dgridfile with the density, second calculate 3dgridfile with QM electrostatic potential (slow), Start up molden, go to the density mode, read in density gridfile map esp on density, Vr icon. -> mapped - fixed bug, after animating normal modes going into the zmatrix editor, clicking one of the variables would move the structure allow a normal mode. - added the reading of multi molecular sdf files. click the 'M' button to select other structures in the sdf file - fixed a bug that would mess up windows on centos, when keeping the pointer over a button and make the help text appear. Thu Mar 5 - fixed bug causes the atoms not to be connected in the density mode in combination with gamess-us and qchem outputs - fixed a bug that would shown an empty structure for orca outout. - surface off would sometimes also switch off some parts of the coil in opengl mode; fixed it Wed Feb 25 - MAYOR: BUG FIX FOR AMBFOR the standalone amber/gaff force field optimizer which is called by molden. The bug caused some torsion force constants to be to big and could lead to distorted optimised geometries. eg anything with a -so4- group. - fixed a bug that would let molden crash when deleting all active structures from the structures window, when the atom attributes window was displayed. - some programs out there write pdb files with lowercase element and residue labels. Molden can now handle these. - fixed a bug that caused read in ambfor .xyz files, to be treated as if they had no charges Thu Jan 15 - added 64 bits executables for linux on our anonymous ftp directory ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/bin/Linux/64bits - fixed a minor bug in the 64 bits version when rendering helices The Dec 18 - Zoom is now kept when editing a zmatrix - Updated the makefile somewhat, let me know if you have problems with it Tue Nov 25 - When a protein was edited via the z-matrix all waters were gone except those with a connection to the protein. Now the waters are restored when exiting the z-matrix editor. - removed a a bug in an earlier undocumented implementation of the above that would make molden crash during the animation of variables in the z-matrix editor. Thu Nov 20 - Added the posibility to color by chains (opengl only). - fixed a bug that would render the molecule as opengl sticks after a HETATM molecule of a protein was removed via the 2nd mouse click popup window. Wed Nov 12 - fixed a bug that could make molden freeze when a help window on a button was activated - fixed a bug with rendering forces and the in/de-crease scale buttons. - fixed a small bug with reading non protein mol2 files, which would cause problems when combining the molecule with a protein structure. - Fixed bug which caused crystal information (biosym car,arc), to be wrongly symmetry expanded if it was not the first structure be read in - fixed a bug that would let molden crash when clicking H-BONDS in the stick mode - fixed a bug that would let molden hang on reading a VASP CONTCAR file - fixed a bug that would let molden crash when as a first file a freq jobs was read in, and consequently the spectrum was displayed. (introduced very recently). Mon Nov 10 - Fixed bug in memory allocation associated with the writing of .ogl files in the surfaces window. When you do a combine between a small molecule and a protein, the memory would be corrupted. fixed it. Fri Nov 7 - Fixed bug writing "charges derived" electrostatic potential mapped surfaces in opengl surfaces window - Fixed minor bug in writing mopac surfaces in density mode in opengl surfaces window Thu Nov 6 - Fixed bug which caused filetypes with crystal information (biosym car,arc) and multiple structures to be treated as containing just one structure. - when only surfaces but no molecule was present in a .ogl, the scene would not be properly displayed. In perspective mode you would be inside the surface with no possibility to zoom in. In the non-perspective mode nothing would be displayed. Fixed it. - fixed bug in new .ogl writing routine, that sometimes wrote too many connections. Tue Nov 4 - when choosing contacts to be displayed followed by a distance measurement, the part of the distance window where the distance should be displyed stayed black, fixed it. - in pdb files with dna/rna the label OP2,OP1 where not supported, now they are. Fri Oct 31 - The newly introduced surfaces window also now allows to write all surfaces to a .ogl file. You can for instance now create several orbitals and write then to a .ogl file - .ogl files ca now be read back in to gmolden. Fri Oct 24 - A new window lets you manage the opengl surfaces created by molden. In the molden control window -> color palette icon -> surfaces You can delete surfaces, change color. Separate helices can now be colored differently. The surfaces window is also available in the denisty mode. It automatically pops up once the opengl icon is clicked. Surfaces can now be activated and deactivated. - The .ogl files when selected in the read file window used longer trigger the launch of the external moldenogl helper program. This behaviour still goes for the Xwindows only version of molden. For the mixed opengl/Xwindows version of molden (gmolden), the .ogl files are dispayed within gmolden itself - Removed a bug that would overwrite the last read file with postscript code, when the character 'p' was pressed in the display window of molden. Wed Sep 17 - The align button in the structures window now also works for small molecules. - When viewing gromacs trajectory the backbone view is maintained if chosen. Also the labels of the cell are no longer displayed in this case. - You can now create a separate structure from the pdb hetatm molecules by clicking with the 2nd mouse button on the drawing screen. This makes it easy to save these molecules in a separte pdb file. - Added cyclopentane and pyrrole as fragments in the zmatrix editor. Fri Sep 12 - Added the option to map the electrostatic potential to the solvent accessible surface Tue Sep 9 - Added the possibility to align proteins Fri Aug 29 - Removed another bug that made the program crash when freeing allocated memory Thu Aug 28 (My birthday :-) - Removed a bug that made the program crash when freeing allocated memory - mol2 files containing multiple structures are now also supported. An extra button (M) in the points section of the molden control window will appear. Clicking this button will allow you to select an other structure in the mol2 file. - Two structures can now be combined. Select a structure, supply a structure number in the field next to the "Combine" button, and click 'Combine'. The structure corresponding to the number will be appended to the active structure. Molden 4.7 first version Aug 22 2008 - Molden4.7 can keep multiple structures in memory. Each time a new file is read in this is a new structure. You can switch betweeen structures in the newly added structure window. The currently selected structure is displayed. You can also delete structures in this window. The original one structure at a time behaviour is still available when specifying the -O command line flag. Molden 4.6 Tue Aug 12 - Fixed a bug when going up one directory (..) in the filemanager. This one managed to escape my attention for a long time. - Minor changes to scrolling Wed Jul 6 - Added dynamic memory allocation voor mopac2007 .aux files Wed Jul 2 - Removed a bug that lets molden crash when you add the first line of a new structure in the z-matrix (windows,macosx) Tue Jun 24 - The mopac2007 .aux format is now supported. The mopac .aux format can hold geometry optimisation data, charges, dipole and orbitals information. The MP6 and RM1 methods have been added in the submit job interface. - Corrected a bug in displaying the dipole moment. Thu May 29 - Activating the picture icon will allways cause a gif image to be written, also in OpenGL mode. The latter requires a 24 bit to 8 bit conversion, which has now been incorporated into molden. For those who would like the rgb picture back, let me know. Tue Apr 29 - Removed bug in gmolden that when adding the first atom in a new z-matrix would make the atom invisible (solid/stick mode only). - Added the ability to cap residues - Added support for neutral asp, glu and lys (ambfor force field) - Improved zmatrix editing of proteins: adding H to histidine will now be recognized as the proper HIS form. Wed Apr 16 - Small annoyance fixes. Switched atom selecting back to the fisrt mouse button again in the atom properties windows. When doing a optimisation, selected atoms now become unselected. Thu Apr 3 - Added small help boxes describing the use of button. If you keep the pointer over a button and dont move, after 1.5 seconds, this helpful window will appear. NOT yet implemented for all windows !! Gradually help for more windows will be added. - Added possibility to close/abort query box - When the user would try to kill the main drawing window by clicking on the x in the border supplied by the window manager, molden would popup a window saying you should kill molden by clicking on the skull button. On some Xwindow servers, this popup window would be off screen. Fixed it. Tue Mar 18 - In the window to specify the atoms and methods for Oniom, the possibility of writing amber charges as part of the element specification for Gaussian has been added. Fri Mar 14 - While reading tinker/ambfor xyz files, a proline could be misclassified as a lysine. The most visible direct effect was strange behaviour of the spline to indicate the coil secundary structure. Fixed. Thu Mar 13 - Labels of Cell axes are now also visible in the opengl mode of gmolden. - Labels of XYZ axes are now also visible in the opengl mode of gmolden. Mon Mar 10 - Fixed bug in 'edit cell parameters' Fri Feb 22 - Added axes, only in gmolden with solid mode. It can be called by pressing '+' or '='. No labels of axes yet: red=x, green=y, blue=z - Added the possibility of calculating molecular surfaces, with help of the program 'surf': ``Linearly Scalable Computation of Smooth Molecular Surfaces", A. Varshney, F. P. Brooks, Jr., and W. V. Wright, IEEE Computer Graphics and Applications, September 1994 [invited submission]. You will find the option under the 'surface' icon -> Mol. surf. This option is mainly intended for use with proteins. Fri Jan 25 - corrected bug in reading molden format files when non integer occupation numbers would be present. Mon Jan 21 - Added reading/writing of CIF files Thu Jan 10 - Added writing of Gaussian cube files (reading was already present). This can also be used to store data on a 3D grid which are slow to calculate. Mon Dec 17 - fixed a bug which could make the automatic z-matrix conversion crash for very small molecules with few connected atoms Wed Dec 12 - Fixed working with nptsx,nptsy,nptsz, edy,edy,edz in combination with opengl - Going to full screen in OpenGL mode would leave the molecule not centered on the ceter of the screen, fixed it. - Refined creating connections between backbone connections. - Refined handeling of unclassified pdb symbols in the ATOM records of a PDB file. - Fog is now automaically disabled in the density mode. Mon Dec 10 - Fixed atom selection by clicking on an atom with the second mouse button while the "Atom Properties window" is open. This functionality was destroyed when introducing the popup window for HETATM molecules on Aug 8 Fri Dec 7 - Atomcolor is now switch on for all but protein structures after reading a new file - Better default setting of shade for proteins Sat Dec 1 - Fixed Molden in such away that it is more compatible with the free Xming Xserver for windows. - Fixed a bug that would let the structure rotate after an buttonpress in the main screen and clicking on of the amino acid options. Fri Nov 23 - fixed bug with displaying G-functions Wed Nov 14 - Added optimisations for displaying the opengl stick & balls for all atoms - added support for gaussian counterpoise optimisations. - added a commandlineflag -S to let molden start with shade off. Fri Nov 9 - Added support for gaussian mp2 optimisations Previously the HF energy would be listed in the geometry convergence window, now the MP2 energy will be displayed. - Added support for gaussian IRC outputs, previously all points were displayed in the geometry convergence windows, now only the optimised geometries along each point of the reaction coordinate. Wed Nov 7 - added a window that lets you specify the total charge when using the EEM charges. - added two new parameter sets to calculate EEM charges with, PESP and ESFF force field parameters - Changed the default for automatically calculating charges for forcefield optimisation with ambfor to PESP. This is because the previous default only had parameters for HCNOF. In addition a string will be printed when no parameters for an element are available. You can always assign charges interactively and switch off automatic charge assigning in the AMBFOR optimise window. - Improved GAFF forcefield typing a bit. - Removed a bug that would occasionally make molden crash when doing a interactive GAFF/Ambfor optimisation and charge labels were also printed (Recursive IO bug). - when the number of atoms exceeded 10000 the writing of tinker xyz files would not print connectivity correctly, fixed it. Tue Oct 30 - added option to interactively change the parameters that determine when molden draws a hydrogen bond. You will find a new entry 'H-bond parameters' under the H icon, the 8th icon from the top from the middle column in the molden control window. Tue Oct 23 - fixed a bug where the reading of Gaussian files would go wrong if the following line was present: RelInt: Using uncontracted basis, .... etc. Wed Oct 17 - added a 'prev' button in addition to the existing 'first', 'next' and 'movie' buttons. - added to molden makefile, the feature to build molden, gmolden and ambfor/ambfor when you type 'make' - added option to convert gaussian log files to zmatrices: gmolden molin contents of file molin: title file=gaussian.log wrzmat=2 The zmatrix will be written in the file called 'zmat.out' - added possibility to scan a part of a proteins rotamer space (max. 6 residues). The best 10 rotamer combinations will be remembered. The initial scoring is done via the dfire pmf score. The output can be saved and (re)loaded via the file 'resrot'. The rotamer combinations can be rescored with the amber force field. To activate the window click on a residue with the second mouse button and select the last option in the menu (add flexible residue). Subsequently do the same for all the residues you want to be flexible. However you first have to create a zmatrix for the protein fisrt by clicking the zmatrix button, otherwise the new option will not be presented. Thu Sep 13 - Fixed bug when applying edited cellparameters - Added option to calculate charges for hetatm molecules from the PDB (in the popup menu, activated with second mouse button click) Fri Sep 7 Fix bug ambfor memory allocation Mon Sep 3 Fixed bug that caused the zmatrix-ordering of atoms to be applied without also changing the charges ordering accordingly, when starting an ambfor (amber/gaff) optimisation. Thu Aug 30 Fixed bug when writing zmatrices bigger than 100 atoms. Wed Aug 29 - improved GAFF typing Thu Aug 23 - fixed a bug that would not display a residue when replaced (in opengl) - fixed a bug that could occur when memory is allocated for proteins larger than 20000 atoms. Fri Aug 17 - fixed bug that displayed "(null)" string when the cursor was above an atom when displaying a non pdb file Tue Aug 14 - fixed a bug that caused molden not to make a correct z-matrix for a pdb file containing nucleotides Wed Aug 8 - added support with ORCA through reading of the ORCA output, currently supported are: single point, geometry optimisation and force/frequency jobs No support for reading electron density and orbitals - Added support for hetatm moelcules from the pdb file, which label will now light up when the pointer is over the hetatm molecule. Clicking the middle mouse button will now bring up a popup menu with options to center on the molecule, create a surface of the molecule and to find neighbouring aminoacids. Mon Jun 11 - Fixed bug in displaying residue labels for pdb files containing DNA - Added the option to have a background color with a gradient. When clicking the 'Palette' icon the first option now is 'Background Mode' You can choose between "solid color" (the way it was) and ' color gradient' To implement this we changed color 13 of the 15 basic molden colors to dark blue, which is used for the default gradient color. Of course this affects the .moldenrc file so you had best remove it and reset your defaults. The background mode is also saved in the .moldenrc file. - Added the reading of electron density maps in the O format (also known as DSN6 format) these are available form the electron density server in Upsala: http://eds.bmc.uu.se/eds/ These maps are only displayed in the OpenGL mode (so gmolden). Wed May 30 - Fixed a bug in writing .mol filee, of elements with a two letter abbreviation only the last was written. - added reading of DSN6 electron density maps, these can be read in from the surface icon -> last option and can be displayed on top of a pdb structure - added information how to compile under gfortran/gcc4.0 and higher to the makefile and molden.f file (uncomment external gfortran_iarc) Fri May 4 - Fixed bug of displaying the dipole moment, the dipole moment was only correctly displayed for single point QM calculations, not QM optimisations. Fixed it. Tue Mar 20 - Removed a bug affecting the processing of biosym .car files. Bug was introduced when adding dynamic memory allocation for protein coordinates - Removed a bug affecting reading of xyz files being added to an existing structure. Bug was introduced when adding dynamic memory allocation for protein coordinates Mon Mar 12 - Removed a bug affecting the visualisation of vibrations of gamess-us and Qchem introduced when adding dynamic memory allocation for protein coordinates Fri Mar 9 - Removed a bug in the processing of gaussian outputs, the bug is 'fixed' but be aware that it is not exhaustively tested as of yet - made a minor bug fix to the reading of QChem output Fri Mar 2 - Performance update: OpenGL density mode now makes less unnecessary screen updates. Only important for working with remote displays. Tue Feb 20 - Created dynamic memory allocation for proteins (all formats that support protein information, pdb, mol2, tinker xyz, .gro) - Display of dipole moment, if QM electron density is available, the QM dipole moment is first calculated, if charges are available (but no QM electron density), the dipole moment is calculated from the charges. - Added possibility to rotate ligand within an active site: The align icon (middle column, 9th from the top) Interactive docking -> Pick molecule from screen -> pick a molecule from the HETATM records of the Pdb file. ------------------------------------------------------------------------ Molden 4.5 Fri Dec 2 - Optimised protein display in the opengl version: - residues now have their own gllist, when you display a whole protien as solid you will see the protein being build up residue per residue. Solid protein display will also display somewhat faster. - when clicking the backbone button you will immediately see the secondary structure elements - animation of variables in the zmatrix editor in solid mode will be a lot faster, also replacing rotamers. - you can now choose between the richardson and dunbrack rotamer libraries Tue Oct 17 - Did some improvements to the QChem interface Thu Sep 7 - Did some optimisation of orbitals and regular density space filling plots. Thu Aug 31 - changed the fortran code so that use of the -O2 compiler flag on linux nolonger causes incorrect display of the surface in xwindows lines mode (the surface looked incomplete) Thu Aug 17 - The opengl version of molden (gmolden) would show dark blue lines in the density-3dgrid mode with certain xwindow emulators. Fixed it so that the lines are white again i Wed Jul 12 - added a button "to Xmgr" which when clicked will right a file with pairs of frequency,intensity on each lines. These files can be imported into xmgr or xmgrace Mon Jul 10 - when displaying vasp POSCAR or CONTCAR files, and there is a XDATCAR file present molden will ask to use the XDATCAR, the multiple structures can be called with the 'fisrt','next' and 'movie' buttons. - when doing interactive docking sometimes extra hydrogens were added to the second molecule with erroneous connections to the first molecule, fixed it. - when doing interactive docking you are now asked if you want to align the centers of both molecules or not (yes used to be the default) - the make option 'make noxwin' now should work again. This can be used to create a version of molden without xwindows and opengl, you can only control this version with a keyword file. Wed Jun 28 - The internal opengl representation of mopac .gpt files had errors in representing the connections of the molecule. - Tinker xyz files which use the amber or charm forcefields are now correctly visualized when atoms like F, P Cl and Br are used. Tue Jun 6 - B. van Eijck added the keyword CHADD, which will read extra charge centers from a 'molden.def' file. Tue May 30 - Removed some small bugs, reported by Robert Gyepes - added a special makefile for cygwin makefile.cygwin Fri May 19 - Added 'best rotamer' option, this calulates for a particular residue, the best scoring rotamer according to the dfire protein-protein score. - Removed a bug which on some platforms would make molden crash when writing out a z-matrix - Some rudumentary support for gfortran (you still have to edit molden.f and comment out the line 'external iargc' ) Wed Mar 8 Spherical G-functions (9G) in combination with electrostatic potential and mulliken charges are now also fully supported Mon Mar 6 - Support for Gaussian cartesian G-functions (previously i was unaware of G-functions in the Gaussian series of packages). - Support for the Gaussian03 revision D, the output format of the basisset has slightly changed. Adpated molden to deal with it. Tue Feb 7 - First support for QChem outputs: For molden to be able to read orbital and basis-set information, supply the following qchem keywords in the $rem section: PRINT_ORBITALS TRUE PRINT_GENERAL_BASIS TRUE You can supply output of composite qchem jobs, molden detects it and will allow you to select the different job outputs by clicking on the 'M' button which appears in the "Select Point:" section in the molden control window. NOTE: support is still rudimentary, i dont have qchem, only a few outputs sent to me by a user. If you think this functionality is important than let me know when it doesnt work Thu Jan 19 - Support for dynamic memory allocation for the part that shows geometry convergence, implemented for use with gromacs and cpmd. - In popop menus you always had to choose a selection (sometimes cancel) Now you can click besides the popup window to get out of the popup and cancel the selection. Therefor the option "Cancel" there where used to be offered has been removed. Tue Dec 20 - Support for the latest Gamess-US version (tested 27 JUN 2005 (R3) version). The basis-set print out of Gamess-US version had changed. Fri Dec 16 - When writing PDB files, in case of no chain information read in molden will now generate and write chain labels - With gromacs files the generation of connectivity is now much quicker also solvent molecules will be rendered in less detail in opengl molden which will speed things up a little Fri Dec 9 - Molden can now read the binary gromacs files .trr and .edr. Previously molden would first convert them to their ascii counterparts with the gmxdump utility. This way the very large ascii files are nolonger needed. Tue Nov 29 - Added molden keyword 'MOGL' which will let you create a molden.ogl file from a molden keyword file. Mon Nov 28 - When replacing one amino acid residue by another, followed by writing a pdb file, the replaced residue number would be wrong: fixed - When writing .mol2 files, sometimes a double bond to many was written (conjugated systems), since molden does not do anything with bond types this was not serious, but other programs (sybyl) do work with bond types. - When Cbeta or backbone O (C=O) was missing on a pdb residue, connections to a non existing atom at cart.coord (0,0,0) would be drawn in the opengl version of molden (gmolden) Mon Nov 7 - With gmolden the aminoacid currently under the pointer is shown by temporarily showing the label, when clicking with the second mouse button a popup window with a few options pertaining to amino acids would appear, every now and then this window would not be visible untill you moved the pointer over it (only on certain xservers), fixed it. Wed Nov 2 - Fixed writing of Gaussian inputfiles for oniom calculations (from the submit Gaussian Job windows). This bug was introduced when charges for proteins were added (amber forcefield) in molden4.1 (Why does no one ever tell me it does not work ???) - Changed the working of the residue commands window: 128-130:A would mean residue 128 through 130 of chain with Label "A" NOW all numbers refer to residue numbers used in the PDB file: 128-130:A now actually means the same as 128-130. You still can use the chain label for things like coloring: *:A col Will let you pick a color with which all residues belonging to chain "A" are colored with this color 128 residue with PDB residue number 128 will be shown. Fri Oct 28 - fixed a bug that would override user assigned sybyl atom types, when writing mol2 files - added the possibility to change the potential levels at which certain colors where used for the colorcoded opengl esp potential - The PC-UNIX version of Gamess-US misses the first column with respect to the regular Unix version, made some adaptation to let molden work with this output to. - Fixed geom conv for a series of xyz structures where so of them had 'heat' 0.0 Fri Sep 30 - reorder Z-matrix, clicking a few atoms and then hitting escape, this would create a zmatrix in the order of clicked atoms and the rest would be figured out by molden. This did not always work. I fixed it in such a way that it can handle nearly all cases but there are still some conditions not supported, but this is not so relevant since you can always do it again. - When doing interactive docking, you can now change the center around which the ligand rotates (in the same way as the overall rotation center). And you can now reorder the z-matrix of the docked ligand. Wed Sep 23 - Added the possiblity to do a surface per residue in the surface window (opengl version only), takes longer but also looks a lot better. - When aligning or docking and then writing as a PDB file some of the atoms were missing, corrected it. - When docking a molecule, the to be docked molecule is placed at the center of the molecule docked to. Wed Sep 21 - Fixed running tinker in the background for the opengl version of molden - Made residue commands concerning surface also work for the opengl version - Added Fit Rotamer option, which will replace the amino acid conformation with the closest rotamer in the rotamer library Mon Sep 5 - Added support for the tinker amoebapro force field - reading in tinker xyz amber files would be retyped to charmm types fixed this Mon Aug 15 - Fixed xwin.c for molden without OpenGL - Fixed writing of GIF files for using Xservers with 16 bit planes Fri Jul 15 - Added interactive opengl support for the density mode (only available with 'make gmolden'). - Fixed bug which can lead to not displaying gaussian outputs correctly in some cases. - Fixed a number of small annoyances (dont worry, there are enough left). Wed Jun 15 - fixed bug that let f-functions run in to the code meant for the g-functions resulting in reporting number of orbitals is wrong - fixed reading MOL files, this bug was introduced with support for reading gromacs files Thu Jun 2 Addition of creating opengl surfaces in the molecular mode, when clicked add to the backbone (protein structure only), and clicking with the second mouse button on a backbone atom a drop menu will appear, which let you do things like (un)display the residue, center it, and add to the surface (of course only available when molden is compiled with opengl support (gmolden)) ------------------------------------------------------------------------ Molden4.4 Mon May 9 The main reasons for this new minor version of molden are: - Introduction of the incorporation of interactive Opengl in the main interface of molden (molden already had opengl helper program moldenogl) You can build the gmolden version by typing; make gmolden This version is still under development - Reading of NLMO's of the NBO analysis in gaussian - Partial support for G-functions. As far as orbitals and electron density G-functions are supported. Also mulliken charges, except when using 9G functions. The electrostatic potential is not yet supported. Addition of a new keyword to the molden format: [9G] which specifies the use of spherical G-functions instead of gaussians. The order in which molden expects MO coefficients to pe printed is: For spherical G-functions: G 0,G+1,G-1,G+2,G-2,G+3,G-3,G+4,G-4 For cartesian G-functions: xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy xxyy xxzz yyzz xxyz yyxz zzxy The request for support for G-function came from the molcas development people, but also Gamess-US will benefit from this support. ------------------------------------------------------------------------ Molden4.3 Fri Apr 29 - introduced number of small bug fixes: the environment g03root was not recognised and g98 was written in the .run files created by molden - premature end of file in gaussian can let molden crash, removed one instance on which it could crash - Introduction of the incorporation of interactive Opengl in the main interface of molden (molden already had opengl helper program moldenogl) You can build the gmolden version by typing; make gmolden This version is still under development - Reading of NLMO's of the NBO analysis in gaussian - addition of dynamic aminoacid labels and clicking on a backbone atom will bring up a small dropdown menu with visualisation options Wed Feb 23 - Fixed bug that effectively disabled the aligning of two molecules - Fixed a bug in the z-matrix editor that would not correctly show all atoms in the when the 'stickcolor' mode was disabled. Fri Jan 28 2005 - Lots of small bugfixes, as there are: Fixed editing z-matrix of ligand when doing interactive docking, Not edit operations where bug free Fixed updating of properties when editing the z-matrix - Added support for the Gromacs (gmx) file format .gro: Molden will read the file name.gro and will then look for the file name.top to read connectivity, charges and atom types. When not found Molden will create connectivity. Next molden will look for a trajectory file name.ttr. If found it will use gmxdump to convert it to an ascii trajectory file name.trra. Molden will not do the conversion if a ascii trajectory file name.trra already exists. Next molden will look for an energy file name.edr. If found it will use gmxdump to convert it to an ascii energy file name.trra. Molden will not do the conversion if a ascii trajectory file name.trra already exists. If a trajectory file is found, then molden can animate the MD run by clicking on the movie button. - Hitting the escape key when running an animation will exit the animation. Hitting the space key will stop the animation and when hit again will resume the animation. Fri Jan 14 2005 - Some more work on the writing of mol2 file for proteins. - Incomplete amino acids are now reported. - changed xwin.c so it does better on 64 bits AMD/Opteron systems. Tue Dec 21 2004 Introduction of Molden4.3: - The reading of Gaussian output files has been restructured, it is possible that this may temporarily be a step back in molden reliablity. PLEASE inform us of any problems related to reading gaussian outputs. - Did some work on writing better mol2 files for proteins, there are still problems, but at least molden can now read it back and create a z-matrix for the protein without crashing. Sybyl still has problems with these files ! It needs more work. - Added forces information to the molden format, example: [FORCES] point 1 3 -0.000038 -0.000160 0.000430 0.000834 0.000150 0.000047 -0.000263 0.000008 -0.000017 point 2 3 -0.000505 0.000339 0.000987 0.001268 -0.000634 -0.000242 0.000123 -0.000017 -0.000640 .... point 10 3 -0.001299 0.000970 0.001904 0.002139 -0.001328 -0.001049 0.000512 0.000004 -0.001636 The number of points must match the number of points used in the [GEOMETRIES] section. Second form includes coordinates, this is only needed when the forces are not in the same orientation as the geometries supplied in the [GEOMETRIES] section. For instance, the Gamess-US forces are not in the z-matrix orientation , so when [GEOMETRIES] ZMAT is used the forces would not be in the correct orientation. [FORCES] COORD point 1 3 -0.000038 -0.000160 0.000430 0.0 0.0 0.0 0.000834 0.000150 0.000047 0.0 0.0 1.0 -0.000263 0.000008 -0.000017 0.0 0.0 -1.0 .... NOTE: this extension is on trial, it may not be the final solution. Developers who write their own molden format should not be overanxious to implement it. - fixed problems with reading circulair peptides. - increased the max number of geometries and scf iterations molden can handle to 2000 and 1000 respectively. ------------------------------------------------------------------------ Molden4.2 Tue Oct 05 2004 - Corrected a few fortran syntax errors, thnx to Gyepes R. - on some platforms molden would not write a z-matrix, after stating that it just did. fixed Thu Aug 05 2004 Molden 4.2 introduces quite some radical changes in the way proteins can be manipulated with the z-matrix editor. Where in previous versions any change to the z-matrix was followed by a complete update of the cartesian structure, with molden4.1 only those parts of the cartesian structure are updated that have actually changed. The advantages are that protein manipulation is much faster and now larger proteins can be manipulated, these manipulations include, deletion, insertion and replacement of amino acids. Also the animation of variables such as the chi sidechain rotamer angles can now be done interactively. A new feature is the possiblity to change side-chain rotamers. The procedure is now: 1) load in a PDB file 2) click the zmatrix button and create a zmatrix for this protein 3) click the backbone button 4) NEW click on the backbone with the SECOND mouse button and a popup window with side-chain commands will appear: B switch on display of this amino-acid, replace amino acid, replace rotamer 5) Switch to full zmatrix to edit individual atoms 6) click in the zmatrix on the Chi1-4 edit boxes with the second mouse button and select "animate", click the edit box again to end the animation. 7) click in the Molden Control window the button "Hetatm" and switch on Helix, Beta sheet, and coil and optionally any hetatm records. 8) click on the Vr icon (7th from the top) and select OpenGL (you need to have the molden opengl helper program installed for this, moldenogl) to get a high quality opengl display of your protein. The z-matrix is only used for manipulation of the protein, a zmtrix of a protein should never be saved, instead the updated result should be stored in PDB file. The disadvantage of this new approach is a much more complicated algorithm, in which undoubtable some bugs have found there way home. ------------------------------------------------------------------------ Molden4.1 Wed Jul 21 - The zmatrix conversion for proteins containing nucleotides has been improved, it will now create a zmatrix. Still No manipulation of nucleotides however. - The windows version of molden now start the opengl helper program mogl, when you click a *.ogl file in the read file window. Thu Jul 15 - Now when you apply the tinker amber force, automatically the charges associated with the atoms belonging to amino acid residues are set. - A user reported that within gaussian03 you can have the condition that you use pure D functions (5D), but use cartesian F functions (10F). Molden did not handle this correctly, it would assume the use of all pure functions (5D and 7F) or all cartesian (6D and 10F). Molden can now handle this mixed use of pure and cartesian D and F functions. This also has ramifications for the molden file format: Previously the default was 6D en 10F, the use of the keyword [5D] would mean 5D en 7F. The new format uses: - default is 6D and 10F - [5D7F] means 5D and 7F - [5D10F] means 5D and 10F - [7F] means 6D and 7F for backwards compatibility, [5D] still means 5D and 7F. - Fixed a bug that would molden not read the Pseudo Potential information of a G03 run (older versions were ok). - Added the [PSEUDO] section to the molden format: [PSEUDO] Fe 1 16 .... This is elementname followed by the number of the atom and the effective core charge. Wed Jun 16 - fixed bug that would let the windows version of molden crash when you go to the density mode without having read in a file (for the benefit of reading gaussian cube files) - Molden now checks whether the contraction coefficient it reads in via gaussian output files and molden format files contain the normalisation of the contracted gaussian. - increased the maximum number of atoms in the density mode from 300 to 2000, this to the benefit of oniom calculations. (this is independend of the max number of basis functions in molden). Wed Jun 9 - Added interactive docking: - start molden with a PDB/mol2 file containing the pocket - Click the icon with the two phenyl rings overlayed: (In the Molden Control window, the nineth icon from the top). Choose 'Interactive docking' - Supply the name of the PDB file containing the ligand. - Follow on screen instructions for rotation/translation - the Docking Score window will appear, when you rotate/ translate the ligand, the PMF score will be updated in this window. - the window also allows you to store and write combinations of rotation/translation of the ligand (pose). The filename pose.xx will be used for written poses. - The AtomInf button lets you display info on the PMF score contributions of a picked ligand atom: click on one of the ligand atoms. The PMF score window will pop-up with a list of the top negative (=favorable) and top positive atom-pair contribution for the slected ligand atom. When clicking on a list entry the corresponding protein atom of the ligand atom - protein atom pair lights of on the screen (clicking again will switch it off). - activating the 'ligand color mode', will color ligand atoms according to the amount the contribute to the total PMF score for the ligand. Thu Mar 25 - In the z-matrix editor, you can now use the second mouse button to select in molecule drawing screen an atom. Now a change fragment popup box will appear to facilitate structure manipulation. - added the ability to read the high level layer orbitals/ basis-set of an oniom calculation. Apparently the orbitals are only printed at the first point, NOT at the stationary point of an optimise run. - improved the interface to run amber within gaussian. Parameters are automatically assigned (for amino acid atoms!) - When using ONIOM with High and Low layers, the charge & multiplicity check went wrong, fixed it. PLEASE LET ME KNOW if you use the oniom interface in molden and have suggestions for inprovement. ------------------------------------------------------------------------ Molden4.0 Wed Mar 17 - When there is an error reading the vectors (orbitals) in gaussian, molden would automatically skip the reading of ESP charges from gaussian. Fixed this. - The print format for ESP charges has changed going from g98 to g03. The new format is now supported. ` Mon Mar 15 Fixed a bug that lets molden think that any file that begins with an empty line is a mopac .gpt file. Mon Mar 1 - Molden didnt correctly parse Gaussian oniom output: corrected it. - Added better support for the MacOS system, by adding an entry to the makefile for the moldenogl program and adding #ifdef statements to the corresponding C code, ogmol.c and silly.c Tue Feb 17 - Fixed the reading of gaussian outputfiles when using the amber forcefield. Fri Feb 13 - Fixed small bug that wouldnt let you display beta orbitals with the molden commandfile. Thu Feb 5 - Changed common block /freq/ in such a way that compilers no longer complain Mon Jan 19 - Fixed a problem with the new Multi molden_format, In case of multiple molecules with vibrational information, this information was not updated. - The name of the file read via the filemananger will now be displayed as the name of the main graphics window. Same holds for named [MOLECULE] sections of a multi molden_format file. - Changed the code of wrzmat.f, this gave problems on some platforms (AIX). Wed Jan 14 - Fixed a bug that presented it self with g98,g03 xyz optimisation of a molecule with more than 50 atoms. When clicking in the geometry optisation window on a point, the shown geometry would be out of sync with the next/movie button geometries. Mon Jan 12 - Fixed a bug that made molden crash every once in a while on LINUX !!! - Reduced the flickering of windows when an other window is moved over it for LINUX. Thu Jan 08 - support for gaussian with pseudopotentials: Now the proper mulliken charges and density are calculated - In rare cases gaussian reduces the number of MO's, making it smaller than the number of basis functions. Molden can now handle this. Wed Jan 07 - fixed bug reading Molden Format files: when reading two Molden Format files after each other and the number of occupied orbitals in the first was bigger, the second file would have the wrong density matrix due to some old occupation numbers being present. - Molden allocates memory for the orbitals dynamically but not so for the basis-set. This could lead to problems with very large calculations. I increased the storage for the basis-set with a factor of 4. - Added new feature to the Molden format: Molden format files can now be concatenated in to one file, provided they are separated by the [MOLECULE] keyword line. In addition each molecule can have a [TITLE] line, example: [MOLDEN FORMAT] [MOLECULE] [TITLE] title molecule 1 .... rest as usual [MOLECULE] [TITLE] title molecule 2 .... rest as usual If Molden reads such a file, a extra button will appear in the "select point" section of the molden control window. When pressed, the titles of the molecule sections will be listed and when selected the appropriate molecule section will be read. Each [MOLECULE] section can have all the previously supported sections/keywords. 2004 Tue Nov 25 - When reordering a Z-matrix nolonger all atoms have to be clicked. When hitting the escape key molden will try to figure out the ordering of the remaining atoms. - Gaussian03 no longer prints just electronic energy during SCF, but total energy, when using the #P keyword. Molden wrongly subtracted the nuclear repulsion energy. Fixed. - Added a button near the "first, next and movie" buttons. When clicked this button will open a window in which the delay time (in milliseconds) between one structure and the next. This delay time also has effect on the display of normal vibrations. Mon Nov 17 - Molden now fully supports 5D and 7F orbitals. Previously, only orbitals and density were supported, NOT mulliken charges, electrostatic potential and multipole expansion. Fri Oct 17 - Via the button "read", there is now the option "add" available as opposed to "replace" which stand for the original behaviour. "ADD" adds a structure to the existing structure on the screen. Currently this option is ONLY supported for the following file types: pdb, mol2, and xyz This option is mainly useful for comparing different conformations (protein) AND offers the ability to read in a protein and overlay different docked ligands. - A mayor overhaul of the PDB editing capabilty via the Z-matrix editor. This will probably need more work, but is quite an improvement over the existing situation. - The Z-matrix editor will now try to keep the original orientation and translation when translating zmat to cartesians. - Molden picks up the normal modes symmetry tag for Gaussian and Mopac output. - prelimenary support for Tinker4.1. Tinker4.1 has different names for the amber and charmm parameters files. Also a few (non residue) atom types have changed, this is NOT YET supported. - use of the gaussian keyword hpmodes caused problems for molden: fixed ------------------------------------------------------------------------ Molden3.9 Tue Aug 26 - calculated spectrum now also supported for mopac Mon Aug 25 - corrected bug that didmt read old gaussian freq outputs Wed Aug 20 - Corrected a bug in the new calculated spectrum part. This bug only manifested itself when the number of frequencies exceeded 200. Mon Jun 30 - Corrected Gaussian03 frequency reading - Now with PDB file writing, the original residue number is maintained - You use an expression like *:A to turn on all residues of the A chain Tue Jun 17 - Added a feature to display an interactive spectrum - Added to the Molden format an item: [INT] intensity1 [raman_intensity1] intensity2 [raman_intensity2] ... intensityn [raman_intensityn] - Added the support for gamess-us Natural orbitals ------------------------------------------------------------------------ Molden3.8 Thu May 22 - Gaussian03 basis-set output has slightly changed with respect to Gaussian98, this would cause error in molden with molecules with more than 9 atoms. Fixed it. Wed May 21 - When forces or displacement were to large, Gaussian would print ******* Molden couldnt deal with that, now it can. Tue May 20 - Support for mopac2000 ASCII gpt files Tue Apr 29 - 3Ddrc gamess-us IRC support Wed Apr 16 - First support for Gaussian03 Tue Apr 01 - PDB residue numbering is now consistent with those in the actucal PDB file - MOPAC grid search output is now somewhat supported - Drawing errors for coil secundary structure are reduced - In the Z-matrix for PDB entries, HETATM's will be attached to the backbone instead of the closest atom. Mon Feb 17 - Added the ability to write MDL mol files. - Added the ability to calculate EEM charges, a sort of gasteiger charges, by Patrick Bultinck - The reading of PDB files now handles additional Hydrogen labels Wed Dec 04 The oniom stuff had a bug for the linux version, fixed. Thu Nov 28 Added an update to the ONIOM window. Tue Nov 05 - Complete update of the Gamess-UK dedicated code by Huub v. Dam: - Reading of SCF-convergence for CASSCF and DFT - Reading of CASSCF orbital occupancies - Support for HESSIAN jobs added - and more ... Thu Oct 17 - Added support for the CPMD program Distributed with the permission of TEODORO LAINO NEST Laboratories - INFM - Scuola Normale Superiore Some work still needs to be done. Fri Oct 11 - Added makefile entry for Mac OSX, thanks to Eric Brown. Wed Sep 25 - Molden3.8 has support for tinker3.9, older versions of tinker are not supported (Molden3.7 support tinker3.6) (Thanks to Nicolas Ferre) - Nicolas Ferre added support for ONIOM calculations with gaussian98. - In submit gaussian window you can specify you want to write cartesian coordinates instead of z-matrix. - You can now run amber from gaussian, in the following way Read in a pdb file, click the z-matrix button and create a z-matrix, assign tinker amber atom types (the FF button) Go to submit job option gaussian, choose method "amber" "Write XYZ" form the "Gaussian Job" window. In principle this can be combined with the oniom method but this is not tested yet. - When introducing Mopac2000 support a bug was introduced which interfered with the reading of tinker xyz files, fixed. Molden3.7 Wed Sep 25 - When introducing Mopac2000 support a bug was introduced which interfered with the reading of tinker xyz files, fixed. Mon Jul 08 - Correction added to the postscript plot. - added F and Cl as hydrogen-bond donors Mon Apr 08 - Gamess-US version 16 FEB 2002, has a slightly different basis-set section. Molden now supports this. Fri Apr 5 - Added support for reading Mopac2000, out and arc files. Wed Mar 20 - added some small changes to the automatic xyz->z-mat conversion Wed Mar 13 - when mol2 files would miss residue information molden would display the structure, fixed - when reading xyz files containing multiple structures containing energy values in the title line, energy values of zero, would not be correctly read on the second time a multiple xyz structure was read. Fixed this. Tue Mar 05 - The introduction of a extra line "FORCE CONST.:" when running a force job with gamess-us, caused molden to not find the normal coordinates. Fixed this. - When running a Gaussian job using F functions, molden incorrectly calculated the ESP charges. Fixed this. - added an option to read the ESP charges calculated by Gaussian Under the surface icon there is a new option "read ESP charges" YEAR 2002 Thu Nov 15 Adapted the script multi_vrml_orbitals.csh to deal with the changed VRML orbitals. Tue Oct 02 The Gamess-UK orbital occupancy section has changed, molden now deals with it. Thu Aug 30 - Assigning sybyl force field atom types sometimes failed to assign aromatic types, fixed it - Now support for different spacegroup setting in mol2 file (the CRYSIN line, setting field (75-142 alternative settings are NOT supported)). - Molden now reads mol files, only 3D tested. The mol file is recognized when the string V2000 or V3000 is present. Wed Jul 25 The Gamess-UK optxyz output has changed, molden gave errors with these new outputs, fixed it. Tue Jul 17 - Added a conversion program to convert CADPAC output to molden format (cad2mol). This program was written by Mariusz Klobukowski (Mariusz.Klobukowski@ualberta.ca). This program is now distributed together with the molden source, to compile it type: make cad2mol To run it: cad2mol 'cadpac_output'.out A file 'cadpac_output'.mdn will be created, molden will be able to read it. Mon Jul 09 - Molden did not allow to subsequent subtractions of 2D grids (gridfile) from the current (density) grid. Rho_AB - Rho_A - Rho_B was not possible. Corrected for it. - Molden nolonger recalculates the density before reading / writing a 2D grid, this make it possible to write subtracted grids. Fri Jun 29 - Added the possibility to render orbitals transparent in VRML2.0 by clicking on them Commandline flag -k adds background + a light. This is to overcome a very dark scene on some terminals. Thu Jun 21 - added small correction to the reading of GAMESS-US outputs (when SCFTYP= and RUNTYP=HESSIAN were not on the same line in the input file, molden would not display the vibrations). Thanks to Georgy Salnikov, NMR Group, Novosibirsk Institute of Organic Chemistry, Russia Thu May 31 - Added support for writing mopac2000 input containing crystal information (Tv vectors) Tue May 15 - Added support for mopac2000 output containing crystal information (Tv vectors) Mon May 14 - Removed a bug in reading pdb files containing just HETATM records. Thu May 10 - REMOVED MAYOR BUG in reading new basis-set section of GAMESS_US !!!!! Thu May 9 - Molden can now launch a G98W session on windows Thu Apr 19 - Addded new makefile section for HP-UX Mon Apr 2 - The Z-matrix editor option "substitute atom by fragment"-> "Read" sometimes passed the wrong filename, fixed it. Tue Mar 13 - Molden sometimes crashed on the OPTXYZ output of Gamess-UK. Fixed thanks to Huub van Dam. Wed Mar 07 - Molden now deals with changed writing o MCSCF orbitals of Gamess-US. - Gaussian98 by default only prints the Z-matrix and resultant coordinates ONLY for 50 atoms or less. However molden didnt respond correctly when this default was overridden with the keyword: IOP(2/11=1). Fixed. Tue Dec 19 -Added Option to specify opt=z-matrix in the "submit job" for Gaussian, available from the Z-matrix editor. This forces Gaussian to use the Z-matrix when optimising. The default is to use a nonredundant set of internal coordinates - Molden should now nolonger crash on empty files Mon Nov 27 Molden format in combination with both alpha and beta spin orbitals gave problems when more than 128 orbitals were present solved it. Tue Oct 31 Added the ability to visualize protein secondary structure elements such as helices,strands and coil with the OpenGL helper program. The procedure is as follows: - you read in your protein - you click the "BackBone" button (If you do not, all of your protein atoms will visible in the OpenGL, making it extremely slow, except for small polypeptides) - you select ligands via the "HetAtm" button No need to select "Helix","Beta","RNA/DNA" or "coil", they will automatically be included in the OpenGL. - select separate residues to be displayed by clicking "Residue" and then clicking on the backbone on the screen. - Decide wether you want the residues and ligands to be displayed as tubes (default) or as spacefilling The latter can be switched on by clicking "Solid" -> "Space Filling" - Decide wether you want the residues and ligands to colored by their elements or by residue/ligand color This is controlled by the "StickColor" button. - Now click the "Vr" icon and select "OpenGL" Molden will create a file called "molden.ogl" and start up the OpenGL helper program "moldenogl" Remember to rename this file if you want to keep it, otherwise molden will overwrite it the next time. - At anytime you can visualize this file again, without having to start molden by typing: moldenogl or: moldenogl molden.ogl - use the moldenogl cammand line flag "-r" is you want to use high quality spheres and cylinders. This will increase the graphics quality at the expense of speed of rotation. - Use the left mouse button to rotate your molecule. In combination with the "Ctrl" and "Shift" button respectively, a zoom and translation are performed. - The third mouse button will bring up menu with lots of option, of which the "Screen Capture" option allows you to save your picture as screen dump postscript or "Vector Postscript". The latter take longer but will yield a better picture on a native postscript printer. - molden has a new commandline option "-z", this will let molden use more polygons and will result in a better opengl picture (at the expense of speed, but ideal for a good postscript picture in combination with the moldenogl -r flag). - you can edit the "molden.ogl" file, specifically the following section is important: [COL STRANDTOP] 0.0 0.0 1.0 [COL STRANDBOTTOM] 1.0 0.0 1.0 [COL HELIXOUT] 0.0 1.0 0.0 [COL HELIXIN] 0.6 0.6 0.6 [COL RNA] 0.5 1.0 0.5 [COL COIL] 1.0 1.0 1.0 This defines the color of the beta strand (first two), the helix outer and inner surface (following two), and the RNA and Coil parts respectively. They are used further down the file: [RIBBON] HELIXOUT Alternatively you may supply a color per ribbon, by supplying rgb triples (red,green,blue): [RIBBON] COLOR 1.0 0.0 0.0 In molden you can now also select "coil". In addition you can click on the helix,strand or coil to activate a residue (in combination with the "Residue" button. Also added the writing of POVRAY files of the ribbon cartoons as desribed above. Follow the same procedure to generate then, except that you have to choose "Povray" under the "Vr" icon. Molden3.6: Fri Sep 15 - Gamess-us (After Jan10 2000) outputs gave problems on 64-bit Alpha-linux systems, corrected it. G77 compiler flag -mieee has to be added. Tue Sep 12 - Added screen capture possibilities to the OpenGL helper program moldenogl. Three options: - IRIS RGB format (key F10) - greyscale encapsulated postscript (key F11) - PPM bitmap file (key F12) added a menu option "screen capture" holding the above three options Thanks to Pedro Vazquez for supplying the code for postscript and PPM writing. Mon Aug 21 - Problem with reading shelx files generated by the CSD's conquest code: SYMM .5+x, .5+y, z Molden expected all capitals, fixed to handle lower case. (All commands must still be in uppercase however). - Trying to edit the cell parameters of a structure read in as shelx file, made the program core dump, fixed. Thu Aug 17 - Added keywords to enable mapping of properties onto a isosurface with Gaussian Cube files, example: title GAUCUB=meto_dens.cube MAPFIL=meto_esp.cube VRML2.0 SPACE=0.001 MAPVAL=(-0.3,-0.1,0.0,0.1,0.3) GAUCUB for the Gaussian cube containing the density MAPFIL for the Gaussian cube containing the property (like the electrostatic potential) MAPVAL use to change the default property values associated with the 5 basic colors used for interpolation (default values: (-0.1,-0.05,0.0,0.05,0.1)) Remember currently mapping only works with VRML2.0 and OpenGL output. - Added a program called 'short_wrl' written by Andreas Klamt of COSMOlogic, to remove redundant vertices from moldens VRML2.0 files To build it type: make short_wrl To run it: short_wrl molden.wrl Now molden.+.wrl contains the new VRML2.0 file Fri Aug 11 - The GAMESS-US basis-set output section has changed molden has been updated to deal with this - Molden now also writes a '[LINES]' section to the molden.ogl file. This is the input file for the molden OpenGL helper application moldenogl. Older versions of moldenogl may have problems with this new section. The [LINES] section has been constructed to visualize the cell and alpha helices and beta strands. - Added a few options to the moldenogl, when clicking with the third mouse button in the main drawing window you find a menu with as new option 'Animation' this options under it will allow you to stop/start the animation, advance by one point (also key 'n' or 'N') and lets you slow down animations. Fri Jun 30 - GAMESS-US has a changed writing when using pure 5D molden now deals with in (Thanks to Fred Arnold) - the moldenogl helper program can now also be called from the 'molecular mode', it will do normal vibration animations and animations of molecular reactions. (Via the VR icon->Opengl). the molden.ogl format now accepts more molecules. Added the option -l,-p,-b number to moldenolg -l = low resolution molecule (faster) -p = perspective mode on -b number = choose background color Added also to the popup menu, including a fullscreen option, and a light2. (three lights 0,1,2) Mon Jun 26 - The routine reading XYZ files had a problem reading actinium 'ac', fixed it - Added a number of things to the opengl helper program moldenogl, accesible via the menu (third mouse button click): + transparency toggle (or 't') + switching on/off of lights 1 through 3 (or '1','2','3') + fullscreen option (or 'f') + perspective mode (or 'p') Thu Jun 15 - Added the possibility to create an isodensity surface colorcoded with the electrostatic potential. Needed are two gaussian cube files or two molden 3dgridfile's (you can create these by clicking 'write grid' after a 'space' calculation. Molden will always create a file called '3dgridfile') Currently only "Opengl" and VRML2.0 output is supported You will need the updated version of 'moldenogl' to view the OpenGL output. For an explanation how to to this see URL: http://www.cmbi.kun.nl/~schaft/molden/mapped.html For an example VRML2.0 file: http://www.cmbi.kun.nl/~schaft/molden/wrl/gamuk.wrl Added to 'moldenogl' opengl helper is a menuitem (Third mouse button click) 'transparency' In the molden file select window, a click on a file ending with the name '.ogl' will bring up moldenogl with this file. Fri Jun 09 - When a job required more than the default 256 orbitals, molden allocated more memory, but as a result the HOMO and LUMO buttons of the xwindows interface nolonger worked correctly. Fixed it. Mon Jun 5 - Jeffrey Frey and James Hess have suggested a small adjustment of the [MOLDENOGL] format. You can now adjust the transparency of a surface by adding a number: [SURF] TRANS 0.75 Wed May 31 - When reading molden format files with more than 256 orbitals, some arrays were overwritten, fixed it. - In z-matrix editor: the check box to specify Gamess-US style z-matrix writing now print a small explaining message when operated Fri May 12 - Molden generated Povray orbitals had swapped colors with respect to VRML and OpenGL orbitals This is corrected. (blue = positive, red= negative) Thu Apr 27 - BIOSYM/MSI car files for non-periodic work again - In z-matrix editor: instead of "clear status all variables" you now get the option to set the status to variable or constant - In z-matrix editor: Added a check box the specify Gamess-US style z-matrix writing - In z-matrix editor: when typing "c" in the main drawing window molden will look for a file "mapfile" which contains coordinates to orient cartesian coordinates after z-matrix -> cartesian conversion Example "mapfile" 1 50.006 81.343 67.412 2 50.599 80.892 66.194 3 49.514 80.759 65.162 Contains coordinates (angstrom) of atoms numbered 1,2,3 Thu Mar 30 - Molden now nolonger always creates the file 'plot' The xwindow interfaces doesnt, here you generate a postscript plotfile by clicking the corresponding button. Only when supply you molden with a keyword file it will create the plot file Thu Mar 23 - Added primitive support for Jaguar cube files No molecular geometry is displayed however. Start molden without a filename on the commandline Go to the density mode, click "Read Cube", chose "Jaguar" supply a filename, then click the "space" button and supply a contour value. Tue Mar 14 - Fred Arnold added support for reading Gamess-us orbital localisation schemes; Pipek-Mezey and Edmiston-Ruedenberg Thu Mar 09 - Changed povray writing didnt work for orbitals, corrected by Fred Arnold Wed Mar 08 - Under edit cell parameters, you can now also specify a spacegroup name, instead of just a spacegroup number. Fri Mar 03 - support for Gamess-us version with long contraction coefficients. Tue Feb 29 - Fred Arnold updated the writing of povray files. Thu Feb 24 - Molden now nolonger dies when you kill one of its windows - Added a restore color options, under the color palette icon Wed Feb 23 - molden used to center a molecule by working on the atomic coordinates directly. Now this is accomplished via a viewing transformation the coordinates are not affected. - In principle now the conversion of a z-matrix to cartesian takes into account the original orientation of the molecule in cartesian space Fri Feb 11 - Added writing of CML molecules (primitive) - With the introduction the new style of rotation there was a clash between the use of control for zooming in and for temporarily escaping selecting of atoms, under the "Reorder Z-matrix" button of the Z-matrix editor Wed Feb 02 - Added dynamic memory allocation for reading mopac .gpt files. - corrected reading of *.ogl files by moldenogl, created with mopac .gpt files. Mon Jan 31 - added commandlineflag to adjust the maximum number of Gif files molden will write (default 100) molden -j 2000 Molden will write 2000 files at the max. Fri Jan 28 - While adding OpenGL support some errors were introduced for the platforms VMS, CRAY and AIX Mon Jan 24 - Full support to view orbitals/density etc. in OpenGL This is accomplished via a helper program called 'moldenogl', this needs to be build separately. (make moldenogl), you need to place this program in a directory which is in the default path, say /usr/local/bin. You can evoke it from the Xwindows interface under the 'Vr' icon, option OpenGL. Molden will write a file 'molden.ogl', which will be read by the helper program. If you want to save this file you will have to rename it before you choose OpenGL again. You can run 'moldenogl' standalone. moldenogl file.ogl This has been tested for Silicon Graphics and linux. The latter needs the MESA graphical library have a look at URL: http://www.mesa3d.org/ You may need to activate the 'LIBSG' line for your platform. HOW TO OPERATE MOLDENOGL: Use the mouse to rotate the scene, drag while holding down the left mouse button. Further one letter commands: Left Mouse button - rotate Left Mouse button + Shift - translate Left Mouse button + Control - zoom in / out Right Mouse button - bring up options m - toggle molecule x,y,z,X,Y,Z - move position of light PS. On linux the mesa libraries are installed in the the directory /usr/local/lib. This may give the problem that moldenogl cant find these libraries, you can remedie this by either copying the libraries to /usr/lib, or setting the environment variable; LD_LIBRARY_PATH, in say /etc/csh.cshrc (setenv LD_LIBRARY_PATH "/usr/lib;/usr/local/lib") You generate .ogl file from a molden keyword file by use of the keyword OPENGL. - added comandline option -t, which will let molden read chem3d style ascii .gpt files (mopac93) - added a threshhold for plotting displacement vectors in the postscript output of a normal mode. You can set it via the -y commandline flag: molden -y 2.0 (default the threshhold is 0.0, every arrow is plotted) Thanks to: Valentin P. Ananikov NMR Group ND Zelinsky Institute of Organic Chemistry Moscow, Russia e-mail: val@cacr.ioc.ac.ru (URL: http://nmr.ioc.ac.ru/Staff/AnanikovVP/molden-t/ PS: the path uses the -t commandline flag, this is now -y) Thu Jan 13 - The color editor didnt work well on linux, fixed it. Wed Jan 12 - Added first primitive support for OpenGL, THE BELOW IS OUTDATED HAVE A LOOK AT THE ENTRY FOR Jan 24 read the makefile on how to activate it. It only works for Silicon Graphics machines and linux machines. The latter needs the MESA graphical library. Currently only a the equivalent of the 3dx mode is available. You can only activate the OpenGL via a molden keyword file, and the use of the keyword 'silly', file 'molin' Title file=test/adf.molf silly homo ./molden molin Use the mouse to rotate the scene, drag while holding down the left mouse button. Further one letter commands: m toggle molecule . zoom in , zoom out x,y,z,X,Y,Z move position of light - Added the another type of molecular rotation model. It is available via a new icon in the lower right corner of the 'Molden Control Window'. In this model you rotate the molecule by dragging the mouse while holding down the left mouse button. Doing the same while keeping the 'Shift' button pressed lets you translate the molecule. Doing the same while keeping the 'Control' button pressed lets you zoom in/out. Wed Jan 05 - Added maxmimum line width selection under: the palette icon, the option: 'shade depth'. Wed Dec 22 - Added depth of shade editor, under the palette icon there is a new option: 'shade depth'. This option has no effect on the solid drawing mode with perspective off, only the stick mode and solid+perspective modes are affected. Tue Dec 21 - Added the ability to edit colors, under the palette icon there is a new option: 'edit colors'. This option will edit the basic 15 colors available in molden. It will write the colors toe the file '.moldenrc' in the users home directory. The use of 'molden -r colorfile' takes precendence over the reading of .moldenrc. To reset to the defaults just remove the ~/.moldenrc file Thu Dec 9 - the WRZMAT keyword now writes the last z-matrix of say a geometry optimisation, instead of the first - added the commandline flag '-=', which causes a gamess-us dialect of gaussian zmatrix to be written, it has the = sign between variable names and values For use with COORD=ZMAT - Gamess-UK6.2 energies of the geometry convergence were not read properly, fixed it Wed Dec 08 - Updated the makefile entry for CRAY unicos, for running the f90 compiler Thu Dec 02 - writing of non-periodic MSI files used atomic units rather than angstroms, corrected it. - When writing postscript in the molecular mode, molden will check for dummy atoms and will ask you if you want to include them in the plot. In the current situation dummies where not plotted. - In the molecular mode you can change the connectivity of the atoms, but not so in the density mode. This proved a problem for people generating VRML orbitals of metal complexes, i have solved this ONLY for the VRML writing: Before it will write the VRML molecule, it will check for the existence of a file called 'molden_connect' (be sure you have the permission to read it, ls -l molden_connect), this file should hold the connectivity of the molecule, per line two number; atom1 atom2 If atom2 is negative, molden will read an extra line with 5 numbers it will average the coordinates of these 5 atoms and create a bond between atom1 (of the first line) and the average over the 5 atoms (of line two), it will use the color associated with the first atom of line two. If you want to average over less then 5 atoms just supply zeros for the remaining atoms (so avg over 3: i1 i2 i3 0 0) DONT FORGET TO REMOVE OR RENAME THE 'molden_connect' FILE AFTERWARDS. - When you select atoms in the Z_matrix to 'cut out' a part of the atoms to create a new z-matrix, properties like atoms types, forcefield types, color, residue and charge are now inherited. Thu Nov 18 - Added keyword POVRAY, to generate the povray file molden.pov - Added support for Ampac style cube files Thu Nov 11 - Fetched some minor problems: - some msi files were not read correctly, fixed - gamess-US, sometimes doesnt end coordinates with an empty line, but with: '...... END OF ONE-ELECTRON INTEGRALS ......' dealt with - the geometry convergence window sometimes didnt update correctly, fixed it + made them smaller (for PC) - when moving atoms in a cell you couldt use the distance button anymore, fixed it Tue Oct 12 - Solved problem when replacing last amino acid Thu Oct 7 - Reading msi files generated stray atoms when H-bonds where present in the msi file, resolved. Thu Sep 30 - First support for GamessUK6.2, now coping with changed orbital writeout - Added Button to the Z-matrix window to make it smaller. - GLX and ASX PDB residues are mapped to GLN and ASN GLX and ASX caused problems in protein z-matrices Mon Sep 20 - fixed bug: when creating a peptide via the z-matrix closing the z-matrix window and then opening it again caused molden to crash. - Added support for MOL2 protein files, small molecules were already supported. - Added support for reading/writing MSI Cerius files, The reading is NOT robust, it will read simple, periodic structures Thu Sep 9 Molden now uses dynamic memory allocation for the size of the grid, this will allow you to read in any size gaussian or vasp cube files. It also allows you to redefine the size of the grid in points from the 'plotplane' window, via the commnds nptsx= nptsy= nptsz= Previously the maximum was nptsx=nptsy=nptsz=61 The molden version created with 'make noxwin' is NOT dynamic. Mon Sep 6 Molden now uses dynamic memory allocation in some parts of the program: - For a z-matrix of a protein (Not for reading a z-matrix of a protein) - For basis-sets larger than 256 orbitals Not done are for instance the maximum size of a grid (which is 61*61*61), so cube files with larger dimensions are still a problem The molden version created with 'make noxwin' is NOT dynamic. Mon Aug 23 Linked Z-mat variables were not updated onscreen. Non bonded atoms in the stick mode were not correctly shown in the postscript output Thu Aug 19 A word of WARNING: Molden3.6 has gone through quite a few drastic changes, it can therefore be expected to have a few bugs introduced, so for the time being use this version at your own risk, and PLEASE report any problems you encounter (schaft@caos.kun.nl) - Improved filemanager, it now also works correctly in directories other that the current. A directory select window has been added. - More labels options: added "pdbsymbol","residue" - Molden now treats any color depth greater or equal 8 as having 256 color cells - Molden "Author" icon has been replaced by the "FF" icon which when clicked pops up the ForceField type assign window. You can still invoke the author window by typing "a" in the drawing window. - Typing "u" in the drawing window, brings molden secondary windows ontop of the drawing window. (This may not work with the gnome window manager). - In the stick drawing mode, atoms which are not bonded used to be invisible, they are now represented as crosses. - When saving a structure as PDB file it will ask you if you want to write the Hydrogens or not. - Under the "H" icon an option has been added to recalculate the H-bonds. - The biggest addon is the pdb to z-matrix conversion, in essence this was already there in the 3.5 version, but was very buggy (there will probably be some more :-)) In the 3.5 version the whole z-matrix of the protein was shown, which is way to much and cumbersome to handle. In 3.6 the default is to create a z-matrix representation which list the aminoacids with its phi,psi and chi angles. You can click on the Aminoacid button and choose from a number of options: Switch On Switch Off Center Contacts Delete Insert Replace The one letter codes are also displayed. You can search with a string of one letter codes. There is a button to go to the "full Z-matrix" Unlike the old behaviour, ONLY variables which were changed on screen are updated in the internally stored z-matrix IMPORTANT: MOLDEN WILL ONLY PROMPT YOU TO CREATE A Z-MATRIX FOR A PDB FILE WHEN IT HAS ENOUGH ROOM TO STORE THE Z-MATRIX, DEFAULT IT WILL ACCOMODATE 1000 ATOMS, NOT ENOUGH FOR MOST PROTEINS. SO YOU HAVE TO CREATE A BIGGER VERSION OF MOLDEN: - edit the file "change_parameter" - replace the body: 1,\$s/maxorb=256/maxorb=1024/ 1,\$s/numatm=150/numatm=300/ by: 1,\$s/maxat=1000/maxat=20000/ - save this file and execute it: ./change_parameter - change_parameter only works on the fortran files you have to edit the C code manually: - edit xwin.c, replace: #define MAXAT 1000 by: #define MAXAT 20000 - save the file, and type 'make' Molden3.5: Mon Jul 19 - Fixed bug which let you not save charges you edited, when you start of with a file which has no charges Thu Jun 17 - removed small bug in rdgaus.f which made some compilers stop. - added the capability to write and read files with custom spherical atom densities to be used in difference density plots (bonds keyword). molden inputfile inputfile: some title file=gaussian_atomic.log genat a file 'basiinf.mbi' will be written, these can be concatenated and read back in to molden, fi: molden -x atomicdens Thanks to Bjoern Pedersen who implemented it. (Bjoern Pedersen, Technische Universitaet Muenchen Institut fuer organische und Biochemie, Bjoern.Pedersen@ch.tum.de) Thu Jun 3 - Added resizebility of the geometry convergence window - Removed SERIOUS BUG introduced Fri May 21 Wed Jun 2 Added commandline opiton -m, which turns off bell sounds Fri May 21 Added scale factor for normal mode displacement vectors in the frequencey window. Fri May 7 GAUSSIAN: - COMPOUND jobs, (optimisation, followed by a FREQ job) should now be oke. - Gaussian98 doesnt print 'input orientation', for a molecule with more than 50 atoms, in this case molden couldnt show intermediate structures of an optimisation run, FIXED. (The problem could be fixed by supplying IOP(2/11=1) but molden now always takes the 'standard orientation' and disregards forces (for more than 50 atoms)) Tue Apr 27 - Support for reading Gaussian cube files via the molden keyword file (new keyword GAUCUB): tlite gaucub=test/test_homo.cube space=0.1 vrml Thu Apr 22 - Molden can write VASP POSCAR files, under the 'cell' icon, 'write' -> 'write VASP', Molden can also read these files (Use always 'direct or selective' keywords fullout) (Use the first line not as title but put the element names in there). Read support is rudimentary; POSCAR files have all atoms lying in the cell, which may give a scattered outlook of the molecule in the cell. Molden can also read the VASP density grid files, although they tend to be too big for the default molden version. Presently only grids which axes are under 90 degrees will be accepted. - Changed under the 'Cell' icon: the seperate write options; 'write DMAREL', 'write SHELX', 'write CRYSTAL95', into one options 'write', which lets you select out these options + 'write VASP' Thu Apr 15 - Molden can now generate Gif's for 24-bits displays Fri Mar 26 - Added Possibility to delete and move atoms in a crystal, under the CELL icon, the last two options. It was already possible to translate the atoms in a cell but this was interactively, the new translate option allows discrete translations (say 0.5 0 0) of selected atoms in the assymetric unit. Fri Mar 5 - Added commandline flag "-geom XXXxYYY-xxx-yyy" where XXX and YYY are the size of the window in pixels, and xxx and yyy are the position of the window in pixels. Thu Mar 4 - Molden can now read Gaussian Cube files: restrictions: - these must be formatted cube files - supported are: density, potential and orbital cubes (orbital cubes only with ONE orbital!) - the grid MUST be rectangular - grid can only be read in the 'density mode' - Molden now also supports grids which dont have an equal number of points in all three directions, and also the radius in the three directions can be different, under the 'PlotPlane' window there are now 6 new keywords available: npts1,npts2,npts3 and edx,edy,edz Molden3.4: Fri Feb 12 - Added support for G98 optxyz output - Added support for Pluton SPF format - Added some aminoacid sequence editing stuff Tue Jan 19 - Tinker optimisation of structures in molden is done in the Z-matrix ordering of atoms, even if the read in structure is a Tinker xyz file. The last case was not handled properly, it is fixed. You can optimise in the original ordering by suppressing the generation of a Z-matrix by using the commandlineflag -a Tue Jan 12 - Fixed bug in writing chemx .cssr files - Fixed bug in creating the super cell - Fixed bug in interpreting molden-format when [5D] was used. - Added calculation of electrostatic energy, a new button 'E q' was added and a field for specifying the residue number (Eq also calculated interresidue electrostatics), both in the 'Atom Attributes Window' this is popped up when you click with the middle mouse button on a atom. Shift Mouse click in the residue field lets you set this residue number to all the atoms you will subsequently select. - Added -R npts commandline flag this allows you to downsize the size of the grid in points. You can compile with a bigger number of maximum points (Use the script 'change_parameter': 1,\$s/mx3d=61/mx3d=200/ to change the grid size, memory is a consideration since an array of the size mx3d*mx3d*mx3d will be used.) Thanks to: Bjoern Pedersen Technische Universitaet Muenchen Tue Dec 1 - Molden treated Gaussian semi-emirical optimisations as single points, fixed it - With Tinker xyz (charmm,amber), the caps are nolonger (faultily) assigned as residues Mon Nov 30 - Fixed bug that makes molden crash on WinNT/95 and linux when a mopac GRAPH file is read and the orbital select window is activated Mon Nov 9 - For the submit gaussian job, molden now also looks for the g98root environment variable. Tue Oct 20 - support for cssr.arc files. Tue Oct 13 - Removed bug introduced Sep 23, which disabled the mapping of files onto the z-matrix - Further integration of wijnand Mooy's xtinker. Mon Oct 5 - Removed a bug which would in some cases now show a structure in the "molecular mode" for Guassian98 files. - Implemented tinker "amber" force field Tue Sep 29 - Removed bug that occured when viewing MO's from MOPAC/VAMP in the "Molecular Mode" created in the "Density Mode"; the connectivity of the atoms would be messed up. Mon Sep 28 - Implemented tinker preferences window. Wed Sep 23 - Implemented, real time structure optimising with tinker mm3 (small molecule) or tinker charmm (proteins). the molecular display is updated with the intermediate structures. At the end a tinker archive file is created. - Support for tinker archive files. - Vrml from the elctrostatic potential derived from charges in the density mode, now shows both positive and negative lobes. - Adding of fragments can now be done at the start of a new z-matrix Fri Sep 18 - In submit job (Gaussian, Gamess) the check for charge and multiplicity gave an error when there was an dummy (X) present. Mon Sep 7 - Added VRML equivalent of the 3D-X plotting mode, first select this mode from the Molden Control Window, then click the "Vr" icon. - Added creation of peptides. Click "ZMAT Editor", select "Substitute atom by Fragment", select "Sequence" and the "Build Sequence Window" will pop up. Select what kind of conformation you want; alfa helix, or beta (sheet) alternatively a turn. This selects the PHI and PSI angles used. You can still change them in the corresponding PSI and PHI fields. Now specify an amino acid sequence by clicking on the residue buttons, a status bar shows the last 16 residues selected. You can correct an error with the "Undo" button. When ready click "Build". Alternatively you can read in a protein file, which should contain per line: '3 letter amino acid code' Phi Psi [Omega] [Chi1] [Chi2] [Chi3] [Chi4] Everything between [] is optional. The files used by tinker to create peptide can be used. Molden will remember the last amino acid added, so that new partial sequences can be added without selecting an atom to which it should be attached. When ready you can write it out as a PDB file, in the "Molden Control" window click "write" select "PDB". You can also write it as a tinker charm file, close the ZMAT-editor, click with the middle mouse button on an atom this will bring up the "Atom Attributes Window", click on The Force Field button and select "Tinker Charmm", now click on the write button int the "molden Control" window and select "Tinker". Tue Aug 25 - Fixed bug that let molden crash on certain pdb, tinker charmm files. Tue Aug 11 - Added support for Gaussian98 - Molden now adds hydrogens to the amino acids and nucleotides of a PDB entry. - Added checking to user selection of atom types, for Tinker MM3 aand Tinker Charmm. Molden3.3: Thu Jul 23 - Added actinide elements, to atoms property editor - Fixed small bug which wrongly switch label button when FFtype was selected. Wed Jul 22 - Fixed bug in code to deal with ADF orbitals (Fabio Mariotti) - Gamess-uk/us uses different sequence of F orbitals than gaussian, molden always did the gaussian way, corrected. Mon Jul 20 - Fixed small bug which prints lots of arrows on a molcular postscript plot when normal coordinates are available. - the ADF routine assumed exponents and normalisation constants read in from a molden format file as written by the ADFrom program to be in atomic units, this was not the case, the routine has been adapted. Tue Jul 14 - By default molden always tries to make a z-matrix if there is none, occasionally it will have to add a dummy atom to accomplish this. This could cause problems reading some of the frequencies of a frequency job. Noe Fixed. Mon Jul 13 - The window that lets you edit forcefield types, is now brought up when you select the label "ForceF.Type" When you click an atom with the middle mouse button as before this window is also popped up, but in addition the labelling is set to "ForceF.Type" - When using "Optimise" from the z-matrix editor it checks wether atoms typing has already been done. - Added some tinker forcefield parameters for acids, and esters to the .key file written when selecting "Optimise with Tinker" Wed Jul 8 - Added almost all spacegroups. - for molecules with no crystal information, it will be generated when you click on the CELL icon - Added reading of biosym arc files, use the movie and next button in combination with the "Geom. Conv." button. - Under the CELL icon, option "edit cell parameters"; you can now change the spacegroup of the cell - FDAT files containing multiple entries can now be viewed with the "Next" button. - Added "fit multipoles" under the surface icon (molden has to be compiled with "make molden.mpfit" for this option) - Added "Optimise xtinker" option under the CELL icon this writes input files for and executes an adapted version of xtalmin, an crystal structure optimiser from the tinker suite of programs. Adaptation by Wijnand Mooij, not yet available in the tinker distribution. Mon Jun 15 - Added plotting of distance monitors to postscript - Added more types for tinker mm3, automatic assigning still restricted to the old types. Thu Jun 11 - Added writing of Chemx(CSSR) files. IMPORTANT !!!!!!! - Fixed BUG in reading GAUSSIAN94 frequency outputs. It was introduced on 11 april 1998. Wed Jun 3 - Added Scrollable scrollbars - Added atom dynamic typing, click with the middle mouse button on a atom. Tue May 19 - Fixed a bug in molden.f which caused some compilers not to compile it. (Introduced at Thu May 14) - Writing of animated vibrations in VRML2.0: molden -w3 test/mopac.freq Click "Norm. Mode" button, select a frequency, say 11 a file "freq11.wrl" will have been written now. Thu May 14 - Added routine to fit multipoles to the electrostatic potential, stuff written by Wijnand Mooij (w.t.m.mooij@chem.ruu.nl), use keyword 'MPFIT' together with keywords described in file 'mpolefit.f' type 'make molden.mpfit' in the source directory to add this feature to molden. - The new Gamess-US prints frequencies a little different which caused molden not to display the right frequencies this is solved Wed May 6 - Milan Hodoscek (xvibs) supplied code to plot normal coordinates as arrows in the postscript plot. EG: molden test/gaussian.freq click on Norm. mode button, choose the frequency, then click on Norm. mode button again, now click the postscript button. You can use the -s commandline flag to scale the amplitudes (eg: molden -s4.0) Mon Apr 27 - Improved the writing of VRML2.0 animations. These are invoked by: molden -w3 geometriesfile Then clicking the "Movie" button. At completion the VRML2.0 file 'movie.wrl' is written. It include a file via the WEB: http://www.caos.kun.nl/~schaft/molden/wrl/animator.wrl You can edit the movie.wrl via and subtitute the EXTERNPROTO declaration by the contents of animator.wrl. Other adjustable parameters are the size of the animation window: Window [2,1] (Within the DEF MOLDEN_ANIMATOR definition). The cycleInterval in DEF MOLDEN_TIMER this is the time the animation should take. Wed Apr 15 - Added possibility to 'read' and 'write' basis set 3D grids, a file 3dgridfile is created. - Added choice of solid molecule draw: "molden radii" (The old molden solid) "vdwaals radii" This on user requests. Tue Apr 14 - Added reading of BOYS localised orbitals for Gamess-US Fri Apr 3 - The non Xwindows version of molden now works again - Crystal visualisation support for chemx .cssr format and biosym .car files - Through the Z-matrix editor you can build z-matrices which have translation or screw-axis symmetry. Read in the repeating unit, then click on "Substitute atom by Fragment" pick "Periodic", pick "Translation" or "screw-axis", specify the number of repeats. Mon Mar 23 - Support for the new(?) gamess_us PC version is has been added. - Added animation of z-matrix variables. - Added writing of POVRAY files Fri Feb 13 - enabled atonnumbering in postscript printing - Electrostatic potential mapped to an isodensity surface is now possible. Also charges derived this way. - Writing and reading of surfaces. - Orbitals can be displayed as surfaces as well Tue Jan 27 - Enabled writing of 'ATOM' records in the PDB format. - Enabled writing of Tinker Charmm files - Postscript files written by molden, now allow the turning of of the zero contour - Molden Postscript supports non solids drawings and shading on these sticks Fri Jan 9 - Added posibility to create a super cell - Added read/write support for the crystallographic SHELX format (LATT 3, not yet supported) Thu Jan 8 - Constants read in from the constants section of a gaussian/gamess-uk input file are flagged as such in the z-matrix editor, constants which have other variables linked to it, are written to the constants section of an gaussian/gamess z-matrix Wed Jan 7 - Fixed small bug in the gaussian output reading routine. When reading frequency output and encountering a 'exceeding maxnum of orbitals' condition, the wrong coordinates were read. Fri Dec 5 - You can now specify the order of atoms in which a Z-matrix is to be created - When working with files which contain crystal information (FDAT,MOL2,MSF) it is possible to map a z-matrix on file onto the cartesian coordinates. Your z-matrix file has to contain extra mapping information, so after the Z-matrix itself you have to supply the keyword 'map' followed a line per z-matrix atom which indicates to which atom it corresponds in the cartesian file. The name of this special Z-matrix file has to be 'mapfile'. You then start molden with the commanline flag -Z: molden -Z test.fdat Mon Nov 24 - removed bug introduced a week ago, that messed up the connolly surfaces - Added distance monitors - Added editing of cell parameters. - Added the possibilty to align two structures: Read in stucture 1. Click the align icon in the center of the molden control window. Then supply the filename of the file containing structure2. Now use the standard ways of rotation,translation and zoom in/out (z-translation) to align stucture2 to structure1. You can also use the origin icon to change the center of rotation in structure2. You can switch between rotating both structures or structure2 by using the Esc key. Use the Tab key to align by selecting three couples of atoms (a couple = atom structure1 (red), atom structure2 (white) - Reading Support for the tinker .xyz format (mm3/charmm) - It is now possible to work with crystals and change the position and orientation of the packed molecuul via the "Cell Rot On/Off" option under the cell icon. You can switch between rotating both structures or structure2 by using the Esc key. At the same time you can change the packed molecule itself via the z-matrix editor. - Molden can now write input files for the Crystal95 package. Basis sets of previous read in gamess/gaussian jobs are transferred to the Crystal95 input. Works of course only on fdat files and mol2/msf files containing crystal structures. - molden -f pdbfile would create connectivity from scratch, however the HETATM records where not dealt with correctly. - You can change 14 of the colors of the color palette "molden -r colorfile", where colorfile could be: atom color(1-15) VandeWaalsRadius, (- = skip) background color(1-15) palette red #CF54FD ... (14 colors) You can continue the last line on the next line when using the "\" character. You can use color names or Hex red-green -blue triplets Wed Nov 5 - Added more spacegroups for use with mol2/msf files. (100 spacegroups supported) - Improved crystal building code - Support for Gamess-US IRC files - Electrostatic potential due to point charges can be calculated/displayed on a connolly surface See Surface icon. - On mopac output the ESP charges are read in when available. - Writing of simple pdb files, via the 'HETATM' record. - Fixed a bug that caused variable names such as 'e1', 'd1' in a z-matrix input to be not handled correctly. Bug was introduced with the introduction of the molden format. Mon Oct 27 - Introduction of the molden_format - fix of molden format on linux Molden3.2: Fri Oct 24 - Introduction of the molden_format, have a look at the "write" button. - Normal modes with a sequence number greater than 99 where not handled correctly - The background color can be set via the molden -r flag, see molden -h; molden -r Mon Oct 13 - Gaussian Beta Orbitals were not always visible specially when read of a checkpoint file: Fri Oct 10 - Support for ADF, an intermediate program which reads ADF's tape21 can produce files readable by molden. This program was developed by Fabio Mariotti from Prof. Alessandro Bencini group in florence. This intermediate program will eventually become part of the molden distribution, but since it is still under development, you should contact Prof. Bencini: Prof. Alessandro Bencini Universita di Firenze Dipartimento di Chimica, Via Maragliano 75/77 50144 Firenze, Italia Tel: 39-(0)55-354841 e-mail: sandro@chim1.unifi.it bencini@dada.it Wed Oct 8 - Fixed bug in Gamess-UK submit job scheme, the proper 'vectors' option was not always chosen. - The Postscript color of the unit cell is now black per default, it can be changed by in the postscript file by setting /cellcol Wed Sep 24 - Added spin density for UHF calculations Use keyword SPINDENS together with IPSI=0 - Improved dmarel interface - Removed multiple expose events on the zmatrix editor Mon Sep 8 - more Gamess-UK version 6.0 support Fri Sep 5 - removed bug introduced day earlier, resulting in an floating exception on at least Linux Wed Sep 3 - Gamess-UK version 6.0, added first support. - Adapted postscript driver to handle editing of atom display radii. Thu Aug 28 - Enhanced atom color editor to atom property editor Now color, vdw and display radii can be altered. Thu Aug 21 - Added Submitting of Gamess-UK Jobs. GAMESS_ROOT has to be set and the 'rungamess' script must be operational. Mon Aug 18 - Added atom color editor. Fri Aug 15 - Removed bug which when molden was started without a file name would cause the molden control window to never pop up, certainly on AIX. - Gamess-US: when using print options to print 'AO MULLIKEN POPULATIONS IN EACH MOLECULAR ORBITAL' molden didnt read the occupancies correctly, resulting in the density to be calculated to low, and mulliken charges to be incorrect, orbitals ok. Fixed it. - Added Submitting of Mopac Jobs, still very primitive. MOPAC_ROOT has to be set Mon Aug 11 - Removed small bug whith respect to the PLANE/ROT versus LINE/CENTER keywords. Using the PLANE keyword the orientation of the calculated rectangle of points is such that, the first atom specified with the PLANE keyword together with the center of the plot lie parallel with Y-plot axis, when LINE/CENTER or even ROT is used this scheme is abandoned. Wed Jul 23 - Added Submitting of Gaussian Jobs, still very primitive. Thu Jul 17 - Fixed bug that was dormant but became serious on a few platforms after introducing reading of mol2 file on July 13. Files would not be correctly recognized. Wed Jul 16 - Added writing of tinker .xyz files. - Added under "XYZ->curr.zmat" in the Z-matrix editor the possibility to optimise a structure with, sybyl quanta or tinker. The corresponding environment variable has to be set first (TA_ROOT, QNT_ROOT or TNK_ROOT) TNK_ROOT is not used by tinker itself, but molden needs it. (eg: setenv TNK_ROOT /compchem/tinker) The mm3 tinker parameter set will be used. Running quanta is shakey. - Removed a bug that applied to Z-matrices automatically generated for XYZ files, changing variables in the Z-matrix would screw up the molecule. Fri Jul 4 - Added writing of Quanta/Charmm MSF files. - Added atom row containing AG etc. in z-matrix editor. Tue Jul 1 - Added reading of Quanta/Charmm MSF files. - You can now optimise you molecule with sybyl from the z-matrix editor. The environment variable TA_ROOT has to be set first. Choose the "XYZ->curr. zmat" button. Wed Jun 25 - Removed two bugs by which seemingly only the OpenVMS version was affected. Mon Jun 23 - The tolerence for partioning multipole expansion in symmetric molecules was to low, leading very occasionally to wrong multipoles, for higly symmetric molecules. Fixed it. Fri Jun 13 - Incorporated reading and writing mol2 files. For protein just coordinates are read. Writing of Mol2 is very primitive, with respect to atom types, and type of bonds is always single. But you can convert fdat to mol2 files this way, including charges, just first calculate charges on a job with the same atom order as the fdat file, then read in the fdat file and write mol2 (you will find it under the z-matrix editor, cartesian coordinates. Only the top-ten spacegroups have been incorporated, so 90 % of crystal structures will be read. Wed Jun 4 - Fixed bug introduced Fri May 30, affecting the proper writing of zmatrices. - Fixed also some bug related with "delete line" in the z-matrix editor, having to do with maintaining the right status of an internal variable(=constant,=variable,=linked) - In mopac DRC calculations the potential energy is now picked up. Fri May 30 - Rotation around the z-axis is now possible in both directions, clicking the mouse in the middle of the screen will give positive rotation, doing the same while holding down the Control or Shift key will give negative rotation - Molden now supports writing of VRML2.0. Apart from the keyword VRML you can now use VRML2.0 The -W commandline flag does the same. The various VRML buttons now let you choose between VRML1.0 and VRML2.0. The -w commandline flag now knows an option 3. When the movie button is pressed a VRML2.0 animation is written (movie.wrl). This can be viewed with a VRML2.0 compliant browser such as Silicon Graphics Cosmoplayer plug-in (free available, also fro PC's). Clicking on the molecule will start the animation. - typing "g" in the display screen will let you read in and XYZ file which will be mapped onto the current z-matrix, provided the number and the order of the elements is the same in both. Tue May 27 - Added interactive choice between mono and color postscript Fri May 23 - Added Pasting of strings capability to query boxes (For now button 3 will do this) - The interactive calculations of: True ESP derived charges (Very Slow) DMA esp derived charges Mulliken Charges Via the Surface button. Thu May 22 - Removed a small bug in calculating the multipole derived electrostatic potential Fri May 16 - Charges are printed in postscript when the label "atom+charge" is active Wed May 14 - VRML of the elctrostatic potential "space" plots are now handled correctly. Tue May 6 - The Z-matrix scrollbar can now be clicked it, it will trigger pageup or pagedown movement. Fri May 2 - electrostatic potential on a connolly surface: When clicking on the color level rectangle in the upper right corner with the second (or middle) mouse button you can change the colors used. - Added keyword DMACH to calculate charges fit to Distributed Multipole Derived electrostatic potential. Tue Apr 29 - the true or multipole derived electrostatic potential on a connolly surface via keyword file now includes a postscript plot (-C to generate color postscript): molden -C molin > molden.out For the true electrostatic potential: molin: ---------------------------------------------------------- title file=test/gamess_us.h2o_631g_opt.out postscript vdws elpot ---------------------------------------------------- The new keywords XANG,YANG and ZANG controls the orientation viewed, usage XANG=45 (45 degrees) - added the EST parameter set for writing input for the DMAREL program. (molden -e) - added a button "H" to undisplay hydrogens, this is handy in combination with the CSD fdat files when displaying multiple cells. Getting rid of the hydrogen gives a clearer view of the crystal packing - Dummy atoms will no longer be displayed in postscript molecule plots. Thu Mar 13 - Molden could already calculate the true or multipole derived electrostatic potential on a connolly surface, also VRML could be generated for this but only interactively, this can now be done with keywords: molden molin > molden.out For the true electrostatic potential: molin: ---------------------------------------------------------- title file=test/gamess_us.h2o_631g_opt.out vrml vdws elpot ---------------------------------------------------- For the multipole derived electrostatic potential: molin: ---------------------------------------------------------- title file=test/gamess_us.h2o_631g_opt.out vrml vdws ---------------------------------------------------------- A file molden.wrl will be written. Wed Mar 12 - Added ability to display a cell with an Xmol xyz cartesian file: After regular atoms add cell points, valid labels: OO,OA,OB,OC,AB,BC,AC,ZZ These cell points must be included in the number of atoms. - The geometry convergence window together with the movie button have been updated: You can now stop a movie by clicking "first", "next" or by selecting a point in the geometry window. The tick marks are adapted so as not to overlap when there are a large number of points. - added a file epint.f.g77, gnu fortran has problems compiling the original epint.f. So before typing "make", copy epint.f.g77 to epint.f. - Linux2.* has problems with Molden (And Gaussian94) this probably due to an operating system bug affecting memory management. - Removed bug in calculating the q31s octupole moment (Only when using D-functions) - Added commandline flag to keep the order of atoms when creating a z-matrix from cartesian coordinates molden -A - Molden now writes an file "esp.xyz" when doing an ESP charges calculation, it contains the atoms +charge in xyz-coordinates - added support for Gamess-UK rhf localised orbitals. - Added beta-test support for DMAREL, a package that can calculate lattice energies from a multipole expansion. New Commandline flags: -E DMAREL input: use coordinates from multipoles -i opt fdat files: opt=1 standardise H-C, H-N opt=2 1 + standardise phenyl rings Other Relevant flags: -A Keep order of atoms when creating a Z-matrix -D opt DMA mode: 0 = atomic sites only (default) 1 = atomic+halfway-bond sites When creating a z-matrix for an optimisation run to be used with DMAREL you must keep the order of the atoms as in the CSD FDAT file and turn of symmetry to keep it this way: molden -A -i 2 azijnzuur.fdat -> azijnzuur.zmat To use the optimised coordinates instead of the FDAT coordinates in writing DMAREL input, use molden -E azijnzuur_opt.out azijnzuur.fdat if you want to use bondcenters as well, molden -E -D 1 azijnzuur_opt.out azijnzuur.fdat If you want to use fdat coordinates with bondcenters, molden -D 1 -i 2 azijnzuur.out azijnzuur.fdat In molden click on the surface button, choose "Multipole Derived", then read in the FDAT file, click on the "Cell" button and choose "Write DMAREL" a file "dmain" will be created. Wed Feb 12 - In the density mode you could zoom in on the plot with the second mouse button, sometimes old plot were mixed with new plots, fixed it. Tue Feb 11 - GAMESS-US: when using the HSSEND keyword to do a normal vibration analysis at the end of a geometry optimisation, the default is to display geometry optimisation information, but molden -H will trigger visualisation of normal vibration analysis. - GAMESS-US: when imaginairy frequencies were present molden would skip the rest of the normal modes in that line of the output. Mon Feb 10 - Fixed bug in the 'space' mode of orbital plotting A space plot consists of the density/orbital-amplitude plotting and the plotting of the molecule in the stick mode. If the density/orbital-amplitude was to low in a slice then also the part of the molecule in this slice was not plotted. (This did not affect the VRML space filling plots) Wed Dec 18 - Incorporated writing of inputfiles for aresp: Using the keyword 'aresp' will let molden write the files 'resp.in' and 'esp.in' Example keyword file: line1: test esp line2: file = water.out espch debug aresp - The keyword occu dint work correctly, fixed Wed Dec 11 - Molden can now do gaussian natural orbitals as generated by the keywords: pop=(naturalorbitals) gfinput iop(6/7=3) - Molden with Gaussian94 and outputs with only cartesian coordinates would say 'reference to an undefined center' but would still work correct, solved Mon Dec 9 - Molden didnt recognise certain Gaussian94 UHF jobs. Resulting in only one set of orbitals being displayed - Dihedrals with a negative value where not properly written as constants in write zmatrix - In zmatrix editor in the line drawing plot mode the molecule become invisible after adding line two this because th view direction was along the axis of the molecule, fixed it. - some mopac output reads would hang - added a little more control over the postscript file Fri Oct 18 Removed following bugs: - GAMESS-US input files with zmatrix and point group C1 failed - PDB file containing only non-protein and non-rna werent handled well - FDAT files with NRAD=0 failed Thu Oct 17 Removed following bug, when building a structure with the zmatrix editor the display would show the mirror image of the real structure. When writing out this structure and then reading it back in to molden the structure would be displayed in the right way. Wed Oct 9 Added the possibility to do a Distributed Multipole Analysis and the calculation of Mulliken charges. For now, Mulliken charges are calculated only for single point Gamess/Gaussian runs. The Distributed Multipole Analysis can be activated by use of the keyword "MOLPOT". Interactively it can be activated either from the "molden control window" by pushing the "surface button" (The 6th icon in the middle of the window) or pushing the "Dens. Mode" button and consequently choosing the plot function "Elec. Pot" in both cases the user is then presented with the choice between the true electrostatic potential and the electrostatic potential derived from a Multipole expansion. The latter is an order of a magnitude faster than the first. Three types of DMA are available, they can be selected via the "-D opt" commandline flag, where opt can have the values: 0 = atomic sites only (default) 1 = atomic+halfway-bond sites 2 = no shift of overlap dens. of conn. atoms NOTE: In previous versions the keyword "MOLPOT" was used with a DMA analysis read from a Gamess-UK outputfile. Use keyword "RDMULT" to get the old functionality. Molden3.1: Thu Aug 29 Calculating the Laplacian via a keyword file, core dumped It has been resolved. Thu Aug 22 - When visualizing csd fdat files in the "multiple cells" problems arose when there were Hydrogen bonds present. This has been resolved. Wed Aug 21 - Support for the laplacian of the electron density, (the trace of the hessian). Two commandline flags were introduced to aid the space type of plots with the laplacian. -L display both neg. and pos. contour in space plot of the laplacian. Default only the value specified with "space=value" will be rendered. -1 use only the lower half of the cubic grid used for the space type plot -2 use only the upper half of the cubic grid used for the space type plot The latter two were introduced to increase the visibility of the inner (enclosed by other surfaces) surfaces. Thu Jul 25 - Corrected a bug which made you have to click buttons twice Fri Jul 12 - Corrected problem with postscript - Electrostatic potential on connolly surface added. Activated by Clicking on the appropriate icon in the middle of the molden control window. Clicking on points of the surface brings of a popup window with its electrostatic potential value. In the upper right corner of the screen there is a color code rectangle, clicking in it lets you change the increment value between different colors. The 'molden -G 0.5' commandline flag controls the spacing between the lines that make up the connolly surface. - Added the capability to write VRML (molden -V filename, specifies density VRML file, default: molden.wrl) - You can now create a Z-matrix with symmetry, use mouse button two in the zmatrix editor, to: - link variables - to make constants - to mark or unmark Molden3.0: Thu May 23 - Corrected problems on some platforms with the fdat format and the reading of XYZ format without the -X flag Wed May 22 - Rotation in the density window is now attached to button one, rotation will proceed until the button is released, cropping is now attached to button two Wed May 15 - Molden now also recognizes XYZ format without the -X flag - zoom in/out will proceed untill the button is released Fri May 10 - Better encapsulated postscript - Better hydrogen bond display for PDB files - support for hydrogens on RNA/DNA pdb. - molden -r fname: read file with per line; atom color(1-15) VandeWaalsRadius, (- = skip) - molden -w opt: write all points of a movie to a file: opt specifies format; xyz(=1) zmat(=2,mopac) Thu Apr 25 - Increased support for CSD .fdat files. Wed Apr 17 - Support for mopac93/6.0 irc output - gamess-uk inputfiles with no variables/constants oke now - added command line flag for switching off automatic cartesian -> zmatrix conversion; "molden -a" Tue Apr 09 - Some platforms dont support the "logical*1" - Enhanced cartesian -> Z-matrix conversion Tue Mar 29 - Support for mopac6.0/7.0 force runs. - Allow to set the background color, via palette icon. Tue Mar 28 - Support for CSD .fdat files, molden -S will generate symmetry positions and a unit cell. - xmol files that used scientific notation (1.0e05) are now also handled well Tue Mar 19 Mopac input files didnt show up in the z-matrix editor fixed it. You read mopac input files as fragment in the z-matrix editor. Fri Mar 15 Added built in GIF writing capability, dropping the use of the external "convert" program from ImageMagick Wed Mar 13 Extended and improved the rotation of the molecule, holding the mouse button down in the center of the graph will invoke rotation around a z-axis Tue Mar 5 A VERY serious bug effected the calculation of the electrostatic potential and esp charges with Gamess-US/UK output. (It was introduced with Gamess-US support nov. 95) esp's from Gaussian were unaffected !! - ESP charges: introduced keywords AXIS-X,AXIS-Y,AXIS-Z They the define the principle axis used in constructing the atomspheres which make up the connolly surface. Sometimes necessary when you want to reproduce symmetry. Wed Mar 4 - support now for dih, -dih variable use when reading Gamess/Gaussian inputfiles. - With Gamess-UK optimise jobs molden would show orbital energies of the first point, instead of the last point, fixed. Mon Feb 26 A number of bug fixes and new features, see also The history of molden2.9: - Added color postscript for Density Display. Triggered by commandline flag -C - Removed bug that would mess up the EUCLID display when clicking the Postscript button. - considerably enhanced reading and displaying of PDB structures. Helix, beta secondary structure information, will by default be read from the PDB file, if not available Molden will calculate secondary structure information. Use "molden -g" to allways force the latter. From the "Residue Command" window this information can be edited. The color postscript rendering of PDB structures has also been dramatically improved. Molden also lets you display parts of the molecule as a connolly surface. - molden now supports pure F/D-functions (7f,5d) - GAUSSIAN: molden now also read orbitals from dft calculations. - Added commandline flag -h, which prints the available options. Molden2.9: Thu Feb 22 - Added color postscript for Density Display. Triggered by commandline flag -C - Removed bug that would mess up the EUCLID display when clicking the Postscript button. - Made postscript file more suitable for customizing. Tue Feb 20 GAUSSIAN: molden now supports pure F-functions (7f) molden only used to read cartesian F (10f) (As with pure D, not yet for the electrostatic potential) With Gaussian92 and older in combination with ROHF all orbitals were printed, Molden now reads all the orbitals. Fri Feb 16 GAUSSIAN: the use of nosymm could lead to problems. Think I've tackled it now. Also the SCF convergence reading when "SCF Done: E(RB+HF-LYP)" was on the output could cause problems. Thu Feb 15 Changed default to Color Postscript for the molecular display. (Color postscript for the density display not yet implemented) Mono postscript can still be generated by use of the commandline flag -M (molden -M) Thu Feb 8 - Removed bug in postscript printing. - PDB: default is now to read secondary structure info from the PDB file, if there is non the info is calculated. Use "molden -g" to allways force the latter. Wed Feb 7 The postscript (color) rendering of protein structures from the PDB has considerably been enhanced Fri Feb 2 Removed small bug affecting only Ultrix versions of molden when displaying dummy atoms in the solid mode. Removed small bug affecting Ultrix,Solaris when adding a fragment in the Z-matrix editor when no line is selected Thu Feb 1 On the rs6000 (ibm,aix) molden sometimes gave annoying run time warnings, such as "C invalid decimal digit" Wed Jan 31 - GAMESS-US: With geometry optimisations, for each geometry point the z-matrix is read from the output. It used to be generated by Molden. To update the coordinates on screen with the coordinates belonging to the z-matrix, push "Aplly current changes to Z-matrix" Supplying "molden -u" will restore the old behaviour. - Removed small bug which caused problems on a Gaussian optimise job on an already optimised geometry (vectors are still a problem in this case) Tue Jan 30 - Added connolly surface's for protein (PDB) viewing. - Added commandline flag to scale normal motions molden -s4 will increase the amplitude of the vibrations times 4 Molden2.8: Tue Jan 25 - Removed small bug in the automatic z-matrix generation - GAMESS-US: not converged optimisations showed a last invalid point, rendering de energy plot useless. - Problems encountered when having more than 200 points in an optimisation or IRC have been dealt with. Tue Jan 23 Gaussian: molden used to generate its own z-matrix for the z-matrix editor (except gaussian input files) Now it retains the z-matrix on the outputfile. (except for "force jobs") Tue Jan 22 Removed small bug in displaying SCF convergence, SCF convergence of last point sometimes not displayed. Thu Jan 18 Provisionally supported gaussian 5d functions. (density only, electrostatic potentials not yet supported) Wed Jan 17 Removed a bug affecting the reading of gamess input files. Wed Jan 16 Added beta sheet solid rendering. Fri Jan 12 Added numbering to atoms on screen for the convenience of the Z-matrix editor (switch on label when in the zmat editor. Added "substitute atom by fragment" capability in the zmat editor, you can also read a gamess/gaussian/mopac input file as fragment. 1995 Thu Dec 21 Added nucleotide support when reading PDB files Thu Dec 20 Removed bug in z-matrix editor which yielded wrong guesses for bond distances for rare atoms Removed bug in z-matrix editor, which in case of a wrongly user supplied value and when the # of zmat lines was less than 9, would garble the zmat-editor screen. Thu Dec 7 Removed a bug which only affected the Sun solaris version. (In the z-matrix editor whilst adding the second atom) Tue Dec 5 MAJOR BUG FIXES: - molden with GAUSSIAN94 UHF showed only alpha orbitals - GAMESS-US UHF geometry optimisation showed no orbitals Thu Nov 30 removed sleep call in inferr.f, caused problems on AIX,linux and openvms. Zmatrix editor now supplies the first fragments Wed Nov 29 On AIX molden hangs after pushing the "space" button, it was caused by a call to sleep, which should return after 2 seconds but it never returns, you have to deactivate this line in file inferr.f GAMESS-US IMPORTANT BUGS: - Scf-Convergence of GAMESS-US outputs would be empty when "* * * INITIATING DIIS PROCEDURE * * *" was on the output. Taken care of. - fixed inproper reading of orbital occupancies. - fixed incorrect handling of normal vibrations > 9 Tue Nov 21 When entering the z-matix editor without having read a file first, an error occured while adding the second atom of a new z-matrix, removed it. Cleaned up z-matrix editor code for monochrome displays. Removed a bug in routine hidedr, only OpenVMS affected. ` Z-mat editor is a little more intelligent now. Fri Nov 10 Protein viewing: removed inconsistency in displaying hetatm records Mon Nov 6 Gaussian-94 users NOW should use iop(6/7=3) instead of iop(6/7=1), the latter option under g94 nolonger prints all occupied orbitals, the first prints all orbitals. Fri Oct 20 First beta support for Gamess-US And both alpha and beta orbitals (UHF runs) are now displayable. Molden2.7: Mon Oct 9 Made minor changes to let the code compile on Linux, the user has to edit file inferr.f before compilation. Thu Sep 28 The distance,angle and dihedral button now display their output in a dedicated window. Wed Sep 27 Support of Gaussian94 output. Fixed bug introduced on Sep 11, which made the gamess vibration animation routines use the wrong set of coordinates. Molden2.6: Tue Sep 26 Support for pdb ambiguity amino acids, asx,glx,his and hydroxyproline (hyp). Also HETATM A.. are now recognised. Added popup box that lets you choose the color of your HETATM molecule. Fri Sep 22 Fixed an important bug introduced on Mon Sep 18. Mon Sep 18 The cartesian coordinates to z-mat converter now WILL produce a z-matrix for molecules containing 3 atoms on a line. Fri Sep 15 Added the capability to write cartesian coordinates from the Z-matrix editor. Thu Sep 14 Fixed a bug that lets molden crash on some systems, in the case of a molecule containing 3 atoms on a line. Fixed a few other unclarities in the z-mat editor, however the z-mat editor still needs a lot of work. The cartesian coordinates to z-mat converter will not produce a z-matrix for molecules containing 3 atoms on a line Mon Sep 11 Single point gamess calculations retain their user specified z-matrix in the z-matrix editor Thu Sep 7 For pdb files only: Made second display type for the solid helix default Added "neigh=r" command in the residu command window. Neigh looks for neighbours at distance r Changed "substrate" to "hetatm" in the molden control window, clicking it will lets you choose which hetatm molecules you want to display Tue Aug 1 Added second display type for the solid helix Mon Jul 24 Display of vibrations for mopac (tested on mopac93) Fri Jul 14 Incorporated calculation of charges fitted to the ElectroStatic Potential (ESP) on a series of connolly surfaces. (Only for gamess/gaussian) (see test/esp.txt) Molden2.5: Fri Jun 30 The compilation of xwin.c caused some problems on non-ansi compiler systems (hp,sun), fixed it. Thu Jan 26 Removed redundant code which made molden eat cpu when it should be idle. Apparently molden plotted inverted molecules, changed it Jan Improved lighting (At least for protein viewing) 1994 Fri Oct 21 Made support for XMOL cartesian format. Use -X flag Thu Oct 20 Changed resolution of postscript molecule plotting, depending on number of atoms. (Plotting proteins was very slow) Eliminated trailing in rotating the molecule. Molden can now generate color postscript for the molecule display by using the -C flag. Tue Sep 22 ZMatrix editor implemented, incorporating a very rudimentary builder. Molden2.4: Tue Aug 16 Scf/Geometry convergence graphs improved and will now display function value when cursor is over the graph point. clicking in the graph will bring up the current point for display Tue Aug 10 Added support for reading Gamess/Gaussian/Mopac inputfiles and Mopac/Ampac arc files. Mon Aug 1 Added listbox to select orbitals, made internal rearrangements for systematic handeling of queryboxes, listboxes Some query boxes now remain on the screen untill a toggle button is pressed Mon Jul 11 Gamess/Gaussian frequencies/Norm. Modes can now be displayed. Molden2.3: Mon Jun 27 Improved shaded plotmode & switched to fully 3D controls Tue May 17 Removed bugs on commandline parsing on some systems Tue Feb 1 handle gaussian92 scf convergence (turned on by #P in gaussian inputfile) Jan 20 Made molden pc X compatible Thu Dec 23 -c0.2 define depth of shading 0.0 is max, 1.0 is no shades Tue Dec 16 removed bug in the H-bond on screen display routine Wed Dec 15 -f with PDB files, forces connectivity to be build by molden by default connectivity between amino acid atoms are read from the PDB file and for all other atoms molden determines the connectivity Fri Dec 3 better handling hbond when more than one chain better spheres, and beter coloring with shade Thu Dec 2 Better atom selecting by cursor. perspective is now uniform from large to small molecules -p10.0 perspective flag Tue Nov 30 Added reading of binary mopac/ampac *.gpt files Fri Nov 26 -ofilename change the default plotfilename='plot' trying to put in spheres with real depth, not satisf. yet -d debug flag Thu Nov 25 bug out of getmul.f, by Dirk Huckriede Nov 10 Dec Alpha version, corrected problems in wrzmat.f ========================================================================= TODO: - improve zmat editor - Density Functional orbitals of Gaussian94 ? - Clean up handling of dummies - Third rotation axis. - Mopac IRC