Number of frames
Number of atoms in frame no. 1.
x, y, z, Z for atom no. 1
x, y, z, Z for atom no. 2
...
x, y, z, Z for the last atom
Number of atoms in frame no. 2.
x, y, z, Z for atom no. 1
x, y, z, Z for atom no. 2
...
x, y, z, Z for the last atom
etc. for all the frames. Different input formats (among them Gaussian
output files) are allowed if
signalled by the user in a (optional) control file (default file extension
".ctl") or by a command-line option. See the
manual
for more information.
To start the program, type moviemol (return). The program will then ask you: Enter coordinate file name: . You can answer, for example: ex1 (return) - and you're in business, looking at the movie of the "ex1.xyz" file! Alternatively, you can specify the coordinate file name as a command-line argument. That is, type instead: moviemol ex1 (return).
You can now start studying the trajectories in detail by rotating the molecules, zooming in the picture, making a hardcopy now and then, or whatever you might fancy to do - just by pressing the appropriate keys on your PC or workstation keyboard. The action of the keys is described in the next section. Note that only if you care to change the program's default settings do you need to read the manual.
You can obtain some help by supplying the command-line option "-h " when starting moviemol: moviemol -h
Help on the key stroke actions can be obtained in moviemol by pressing the "?" key (when the cursor is located in the moviemol-display window).
Usage:
moviemol [ options ] coordinate-file [ control-file ]
Options:
-help Display this help text.
-nohbond Do not display hydrogen bonds.
-hbond Display hydrogen bonds (the default).
-g94 The coordinate file is a "Gaussian94" output file.
This is the same as -inputformat 21 (see below).
-Zxyz The coordinate file format is Z,x,y,z instead of x,y,z,Z.
This is the same as -inputformat 3 (see below).
-nZxyz The coordinate file format is name,Z,x,y,z (name=char*4).
This is the same as -inputformat 4 (see below).
-Xmol The coordinate file format is similar to that for "Xmol":
number of atoms in frame 1/line of text 1/name,x,y,z of
atom 1 in frame 1/... Same as -inputformat 31
-crystal The coord file contains cell data a,b,c,alfa,beta,gamma
(on the line above #atoms) and fractional coordinates.
-frameno Display the frame number.
-stdinp Read coordinate data from standard input.
-monochrome Monochrome display.
-masterctl Use file as default control file.
The following flag options require an integer parameter. Please see
the manual for a description of each variable.
-icloseopen where = 0 (default) or 1
-icolorps where = 0 or 1 (default)
-idisplaycell where = 0 (default) or 1
-idumpscreen where = 0 (default), 1 or 2
-iframetext where = 0 (default) or 1
-ifixsymbol where = 0 or 1 (default)
-ikeepbonds where = 0 (default) or 1
-imonochrome where = 0 (default) or 1
-inputformat where = 0 (default), 1-4, 10, 11, 21 or 31
-ipersp where = 0 or 1 (default)
-iportrait where = 0 or 1 (default)
-iusedirect where = 0, 1 (default) or 2
-iunit where = 0, 1 (default), 2 or 5
-nframein where = nframes (default) or new #frames
-npixwinx /-npixwiny where = X-window width/height
-nshow where = 1 (default) or new frame interval
To create these movies, you will need a shell script named 'XtoPPM' (which must be executable!) in your current directory. This shell script should contain the lines:
# Shell script to make screen dumps and ppm files in moviemol xwd -nobdrs -name moviemol -out $1 cp $1 moviscrdump.xwd xwdtopnm moviscrdump.xwd > $1 rm moviscrdump.xwdYou will also need to add a line in your moviemol control file ("name.ctl"):
$CNTRL
idumpscreen = 1,
$END
This tells the moviemol program to call the XtoPPM shell script for each
frame. The XtoPPM shell script makes a screen dump of the moviemol
X-window, and transforms the screen dump file into a portable pixmap
("ppm") file. This transformation requires that the 'xwdtopnm'
program from the
"pbmplus" or the
"netpbm"
image-conversion toolkits has
been installed on the computer (I only got it to work using pbmplus, not
netpbm, when I tried it on an IBM Risc workstation - no idea why).
After moviemol has been run using the control file above, a set of ppm files will have been created. These ppm files can then be strung together with the help of the mpeg_encode program (which needs the input file "name.param" in which one has to edit the output file name and the number of frames). The resulting mpeg movies can now be displayed with the mpeg_play program (and can for example be included in your WWW home page).
Some example files can be found in ifm.liu.se/pub/Compchem/moviemol/mpeg_dir.
Additional note: you may also want to add some more lines to your moviemol control file:
$CNTRL
idumpscreen = 1,
npixwinx = 320, npixwiny = 226,
idumpstart = 5, idumpstop = 100, idumpdelta = 5,
$END
The second line in the cntrl namelist makes the X-window smaller
(and so the mpeg files). The third line says that moviemol should start
making screen dumps on frame 5 and stop on frame 100, with an interval
of 5 frames. If idumpscreen=2 screen dumps will occur
when the key P is pressed.