-a no automatic cartesian -> zmat conversion -b use orbitals of first point on opt. runs -c0.5 change depth of shading -d print debug information -e DMAREL INPUT: Use est set of parameters -f PDB: build connectivity from cartesian coordinates -g PDB: always calculate Helix/Sheet information -h print commandline flags -hoff switch of hydrogen bonds -hdmin x mininum hydrogen bond distance (Ang) -hdmax x maximum hydrogen bond distance (Ang) -hamin x mininum hydrogen bond angle (Degrees) -hamax x maximum hydrogen bond angle (Degrees) -i opt fdat files: opt=1 standardise H-C, H-N opt=2 1 + standardise phenyl rings -l dont display molden logo -oppp change default plotfilename from 'plot' to 'ppp' -o ppp -p2.0 change default perspective value from 0.3 to 2.0 -r fname read file with per line; atom color(1-15) VandeWaalsRadius, (- = skip) -s4.0 scale amplitude in normal vibrations -u With GAMESS-US optimisation output, molden generates a z-matrix, instead of reading from output -v print verbose information -w opt write all points of a movie to a file: opt specifies format; xyz(=1) zmat(=2,mopac) VRML2.0(=3) -A Keep order of atoms when creating a Z-matrix -C Color postscript (default=mono, except for PDB) -D opt DMA mode: 0 = atomic sites only (default) 1 = atomic+halfway-bond sites 2 = no shift of overlap dens. of conn. atoms -E DMAREL input: use coordinates from multipoles -G 0.6 Grid width colour coded ESP potential map -H GAMESS-US: do normal modes when HSSEND=.TRUE. -L display both neg. and pos. contour in space plot of the laplacian -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 -M MonoChrome postscript -P PDB: treat all input files as PDB files -X When reading XMOL cartesian format -V fname VRML density filename -W Write VRML2.0 instead of VRML1.0 -Z Map the Z-matrix file mapfile onto crystal mapfile contains Z-matrix followed by keyword MAP and per line an integer that maps a Z-matrix line onto a cartesian line