-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 -geom XXXxYYY-xxx-yyy XXX and YYY are the size of the window xxx and yyy are the position of the window -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 -j num maximum number of gifs to write -k num select color of labels (0-15) (gmolden only). -l dont display molden logo -oppp change default plotfilename from 'plot' to 'ppp' -n dont add hydrogens to PDB fil -m turn off the beep sounds -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) -x file read in file with spherical atomic densities -y 1.0 threshold for printing displacement vectors of normal modes to postscript file -z create high quality opengl coils -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. -I dont use shaders, if available -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 -N Check for mpi, to run ambfor/ambmd in parallel -O switch off multiple structures handling -P PDB: treat all input files as PDB files -Q support for older StarNet xwin32 (ver. 6) -R npts adjust the gridsize in points -S start with shade off -T treat all input files as TINKER xyz files -U do not use opengl shaders -V fname VRML density filename -W Write VRML2.0 instead of VRML1.0 -X When reading XMOL cartesian format -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 -= Use gamess-us dialect of gaussian zmat writing