X-Git-Url: http://git.hungrycats.org/cgi-bin/gitweb.cgi?p=xscreensaver;a=blobdiff_plain;f=hacks%2Fglx%2Fmolecule.man;fp=hacks%2Fglx%2Fmolecule.man;h=0000000000000000000000000000000000000000;hp=6ec8328d6d2364e11fc7c13201f461f68e557fbc;hb=019de959b265701cd0c3fccbb61f2b69f06bf9ee;hpb=2762a7d7cf8d83e68b8f635941f6609119d630ae diff --git a/hacks/glx/molecule.man b/hacks/glx/molecule.man deleted file mode 100644 index 6ec8328d..00000000 --- a/hacks/glx/molecule.man +++ /dev/null @@ -1,160 +0,0 @@ -.TH XScreenSaver 1 "13-Mar-01" "X Version 11" -.SH NAME -molecule - draws 3D molecular structures -.SH SYNOPSIS -.B molecule -[\-display \fIhost:display.screen\fP] [\-window] [\-root] -[\-visual \fIvisual\fP] [\-delay \fImicroseconds\fP] -[\-wander] [\-no-wander] -[\-spin \fIaxes\fP] -[\-no-spin] -[\-timeout \fIseconds\fP] -[\-labels] [\-no-labels] -[\-titles] [\-no-titles] -[\-atoms] [\-no-atoms] -[\-bonds] [\-no-bonds] -[\-shells] [\-no-shells] -[\-molecule \fIfile-or-directory\fP] -[\-verbose] -[\-wireframe] -[\-fps] -.SH DESCRIPTION -The \fImolecule\fP program draws several different representations of -molecules. Some common molecules are built in, and it can read PDB -(Protein Data Base) files as input. -.SH OPTIONS -.I molecule -accepts the following options: -.TP 8 -.B \-window -Draw on a newly-created window. This is the default. -.TP 8 -.B \-root -Draw on the root window. -.TP 8 -.B \-install -Install a private colormap for the window. -.TP 8 -.B \-visual \fIvisual\fP\fP -Specify which visual to use. Legal values are the name of a visual class, -or the id number (decimal or hex) of a specific visual. -.TP 8 -.B \-fps -Display the current frame rate, CPU load, and polygon count. -.TP 8 -.B \-verbose -Print debugging info on stderr about files being loaded, etc. -.TP 8 -.B \-wander -Move the molecules around the screen. -.TP 8 -.B \-no\-wander -Keep the molecule centered on the screen. This is the default. -.TP 8 -.B \-spin -Which axes around which the molecule should spin. The default is "XYZ", -meaning rotate it freely in space. "\fB\-spin Z\fP" would rotate the -molecule in the plane of the screen while not rotating it into or out -of the screen; etc. -.TP 8 -.B \-no\-spin -Don't spin it at all: the same as \fB\-spin ""\fP. -.TP 8 -.B \-labels -Draw labels on the atoms (or the spot where the atoms would be.) -This is the default. -.TP 8 -.B \-no\-labels -Do not draw labels on the atoms. -.TP 8 -.B \-titles -Print the name of the molecule and its chemical formula at the top of -the screen. -.TP 8 -.B \-no\-titles -Do not print the molecule name. -.TP 8 -.B \-atoms -Represent the atoms as shaded spheres of appropriate sizes. -This is the default. -.TP 8 -.B \-no\-atoms -Do not draw spheres for the atoms: only draw bond lines. -.TP 8 -.B \-bonds -Represent the atomic bonds as solid tubes of appropriate thicknesses. -This is the default. -.TP 8 -.B \-no\-bonds -Do not draw the bonds: instead, make the spheres for the atoms be -larger, for a "space-filling" representation of the molecule. -.TP 8 -.B \-shells -Draw transparent electron shells around the atoms. This only works -if bonds are also being drawn. -.TP 8 -.B \-no\-shells -Do not draw electron shells. This is the default. -.TP 8 -.B \-shell\-alpha -When drawing shells, how transparent to make them. Default 0.4. -.TP 8 -.B \-wireframe -Draw a wireframe rendition of the molecule: this will consist only of -single-pixel lines for the bonds, and text labels where the atoms go. -This will be very fast. -.TP 8 -.B \-timeout \fIseconds\fP -When using the built-in data set, change to a new molecule every -this-many seconds. Default is 20 seconds. -.TP 8 -.B \-molecule \fIfile-or-directory\fP -Instead of using the built-in molecules, read one from the given file. -This file must be in PDB (Protein Data Base) format. (Note that it's -not uncommon for PDB files to contain only the atoms, with no (or -little) information about the atomic bonds.) - -This can also be a directory, in which case, all of the .pdb files in -that directory will be loaded. A new one will be displayed at random -every few seconds (as per the \fI\-timeout\fP option.) -.PP -When the molecule is too large (bigger than about 30 angstroms from -side to side), the \fI\-label\fP option will be automatically turned -off, because otherwise, the labels would overlap and completely obscure -the display. - -When the molecule is around 150 angstroms from side to side, wireframe -mode will be turned on (because otherwise it would be too slow.) -.SH ENVIRONMENT -.PP -.TP 8 -.B DISPLAY -to get the default host and display number. -.TP 8 -.B XENVIRONMENT -to get the name of a resource file that overrides the global resources -stored in the RESOURCE_MANAGER property. -.SH SEE ALSO -.BR X (1), -.BR xscreensaver (1) -.PP -Documentation on the PDB file format: - - http://www.wwpdb.org/docs.html - http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html - -A good source of PDB files: - - http://www.umass.edu/microbio/rasmol/whereget.htm - http://www.wwpdb.org/docs.html -.SH COPYRIGHT -Copyright \(co 2001-2005 by Jamie Zawinski. -Permission to use, copy, modify, distribute, and sell this software and -its documentation for any purpose is hereby granted without fee, -provided that the above copyright notice appear in all copies and that -both that copyright notice and this permission notice appear in -supporting documentation. No representations are made about the -suitability of this software for any purpose. It is provided "as is" -without express or implied warranty. -.SH AUTHOR -Jamie Zawinski