PD Dr. Stefan Immel - MolArch+ Programs and Program Options

This list gives a short description on the various programs and sub-systems and their program options contained in the MolArch⁺ distribution.

MolArch⁺ - Programs and Sub-systems
Binaries	After having completed the MolArch⁺ installations and settings you will find the following programs (default location at "/usr/local/bin") on your system: *molarch+: Main program MolArch⁺* with a graphical interface and command line. *molarch-: Program version of MolArch⁺* without graphical interface (command line only) for faster batch-processing of multiple molecular files. This is particularly useful for creating animations of molecular ensembles with many video frames. *molarch++* and *molarch- -: Similar to the basic versions above, but with increased limitations on the number of objects that may be handled (larger array dimensions of internal variables), but with a much higher memory demand. molsurf+: Program for generating triangulated Connolly surfaces of molecules. This external program may be called from within MolArch⁺. The helper programs and shell scripts molsurf[0-3]* are used internally by *molsurf+. molcont+: Program for generating 3D triangulated iso-contour surfaces on grid data such as GAUSSIAN* cube files (external program that may be called from within MolArch⁺). *molview+: Program for viewing, superimposing, and printing VOGLE-graphics objects generated by MolArch⁺. It is mainly used to create high-resolution black-and-white graphics. molconv+: Shell script for the simplified creation of high-resolution black-and-white graphics using molview+. molseries+: Shell script for batch-processing of MolArch⁺* script files. *molsymm+: External program used by MolArch⁺* to analyze molecular symmetry.
MolArch⁺ - Program Options
*molarch+*	For a list of program options see: molarch+ -h Usage: molarch+ -[options] --command1 .... --command2 .... Valid [options] are, or correspond to the following commands: -o, -O : Set out-messages off/on -e, -E : Set error-messages off/on -s, -S : Set system-messages off/on -c, -C : Set colored (highlighted) help messages on/off. -H : Disable save history. -d : No graphical display (use as option only, stdin is tty) -l : Switch off the 'molarch+ logo -n : Ignore all set-up files '(.)molarch+' and '(.)molarch+.spr' -D<n>: Debug level <n> (default:0, >1 print debug messages) -h : Display (this) help message and exit -V : Display program version and exit All options are silently executed before all other set-up and initialization files - They may be used to set silently the program defaults and its behavior. The files '(.)molarch+' and '(.)molarch+.spr' are executed (in that order) later and may override options again. Use these options mainly for suppressing all program output (stdout and stderr) and/or running molarch+ without graphic interface, or generally to pre-set non-default behavior (for general information on start-up and initialization files and their locations, see the file *$MOLARCH/molarch+.hlp* the paragraph titled 'Files required').
*molarch-*	For a list of program options see: molarch- -h This is the non-graphics version of '*molarch+*', for the list of command line options see above.
*molarch++* *molarch- -*	These are expanded-array versions of '*molarch+' and 'molarch-*', for the list of command line options see above.
*molsurf+*	For a list of program options see: molsurf+ -h Usage: molsurf+ [-hkqV] [-d <dot-density>] [-r <probe-radius>] pdb-file(s) ... -d <density>: Use dot <density> for the generation of the surfaces (default: 10, allowed range approx. 3 - 50). -r <radius>: Use probe-radius <radius> for surface calculation (default: 1.4 A, approx. size of a single water molecule). -q : Quiet mode - suppress all output. -k : Keep temporary files TMP_SURFACE. -h : Display this (help) message and exit. -V : Print version number and exit. This script creates Connolly-type surfaces (sld-files) for molecules (pdb-files); it uses the 'molsurf0' script, and the programs 'molsurf1', 'molsurf2', and 'molsurf3*'.
*molcont+*	For a list of program options see: molcont+ -h Usage: molcont+ [options] contour-file ini-file out-file-basename Valid [options] are: -f Fast contouring without surface geometry checks (default). -F Full surface geometry checks (slow), this may also be done with the 'molarch+' command 'heal-surface'. -h Display (this) help message and exit. -V Display program version and exit. This program does contouring of 3D (orthogonal) data sets and probability densities.
*molview+*	For a list of program options see: molview+ -h Usage: molview+ [--help] [-rv/--reverse] [-d/--device <output device>] [-q/--quiet] [-w/--width <value>] [-h/--height <value>] [-s/--sector <xmin> <ymin> <xmax> <ymax>] [object-file1] [object-file2] ... Valid options are: -rv/--reverse Set background color to white (default: black). -q/--quiet Quiet execution of program. -s -w -h Set window sector (in A) to be displayed. -d/--device Output device can be: X11 (default), postscript, ppostscript (portrait), cps (color postscript), pcps (color portrait postscript), hpgla1, hpgla2 (or hpgl), hpgla3, hpgla4, dxy, tek. -h Display (this) help message and exit. -V Display program version and exit. Application to visualize (convert into images) and print 'object-files' saved by '*molarch+*'. Use the following statement to convert object files into postscript files and these into pictures: molview+ -q -rv -d pcps [object-files] > [postscript-file] or gs -q -sDEVICE=<device> -r<XXX>x<YYY> -dNOPAUSE \ -sOutputFile=[image-file] -- [postscript-file] Here, <device> is preferably one of these: pcxgray jpeggray pgmraw pgnraw pnggray; for a comprehensive list of available devices see 'gs -h' on your system. <XXX> and <YYY> sets the image resolution in dpi. Or use (skip the postscript output): molview+ -q -rv -d pcps [object-files] \| gs -q -sDEVICE=<device> \ -r<XXX>x<YYY> -dNOPAUSE -sOutputFile=[image-file] - A shortcut is (see below): molconv+ [postscript-file] [object-files]
*molconv+*	For a list of program options see: molconv+ -h Usage: molconv+ [-a(crop)] [-d <device>] [-r <resolution>] [-i(nverse)] [-x <display-width>] [-y <display-height>] [-q(uiet)] [-h(elp)] [-V(ersion)] output-file input-file(s) Valid options are: -a : Auto cropping of borders by 'xv' -d : Ghostscript output device (preferably use one of the following: pcxgray (default) jpeggray pgmraw pgnraw pnggray; for a comprehensive list of available devices see 'gs -h' on your system). -r : Picture resolution in dpi. -i : Set background color to white (default: black). -x : Set display width to <display-width> Angstroms. -y : Set display height to <display-height> Angstroms. -q : Quiet execution of program. -h : Display this (help) message and exit. -V : Print version number and exit. Convert all object-meta-files <input-files> saved by 'molarch+' into a picture with the <resolution> in ppi (pixel per inch), and save the picture (<device>-format, e.g. ppm, pcxmono, pcx256, ...) as <output-file> (Default values: <device>=pcxgray, <resolution>=300).
*molseries+*	For a list of program options see: molseries+ -h Usage: molseries+ [-hV] spr-file arguments ... Valid options are: -s : Pipe file through 'sh' rather than 'molarch+' -h : Display this (help) message and exit. -V : Print version number and exit. For each argument the token $1 or $FILE in the spr-file will be substituted and molarch+ is called with the new spr-file.
*molsymm+*	For a list of program options see: molsymm+ -h Usage: molsymm+ [option value ...] [filename] Valid options are: -verbose ( 0) Determines verbosity level All values above 0 are intended for debugging purposes -maxaxisorder ( 20) Maximum order of rotation axis to look for -maxoptcycles (200) Maximum allowed number of cycles in symmetry element optimization -same ( 0.001) Atoms are colliding if distance falls below this value -primary ( 0.05) Initial loose criterion for atom equivalence -final ( 0.0001) Final criterion for atom equivalence -maxoptstep ( 0.5) Largest step allowed in symmetry element optimization -minoptstep ( 1e-07) Termination criterion in symmetry element optimization -gradstep ( 1e-07) Finite step used in numeric gradient evaluation -minchange ( 1e-10) Minimum allowed change in target function -minchgcycles ( 5) Number of minchange cycles before optimization stops Input is expected in the following format: number_of_atoms AtomicNumber X Y Z ... This program analyzes molecular symmetry.

MolArch+ - Programs and Program Options

MolArch⁺ - Programs and Program Options