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From: |
Chris Harwell <charwel &$at$& chrs1.chem.lsu.edu> |
Date: |
Thu, 12 Jun 1997 09:32:46 -0500 (CDT) |
Subject: |
CCL animation summary (text) |
here is a text version of the animation responses. thank you very much for
contributing!
sorry if anyone had a problem w/ MIME (this ver. of pine does that
automatically w/ all attatchments).
Frits Daalmans sugested that we tar and gzip all mail on the list to save
bandwidth - but i think that may be going a little too far :>
Chris Harwell charwel - at - chrs1.chem.lsu.edu
"Everything positive originates in a positive attitude from someone" :>
Simple Animation Links for Atoms & Molecules
These are in responce to a CCL query for a program to animate pictures of
molecules and change color (to represent charge) during the process.
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* Spartan http://www.wavefun.com
This seems to be do-able in unix Spartan (supports AIX4.1) which
is commercial. The molecular builders allow you to construct the
molecules one by one, and then you group them together as a list. The
list dialog has animation feature to scan through the list frame by
frame. Color information can be altered by users.
* Rasmol http://www.umass.edu/microbio/rasmol/
Rasmol 2.6 has a minor fix (SET WRITE ON) that allows reading a
series of atom coord files and writing corresponding .ppm files within
a script; the .ppm files can be made into an MPEG animation using
mpeg_encode. There does seem to be a limit on either the number of text
lines in a script, or the number of coordinate files read, etc. within
Rasmol. I've appended a partial example .
* VMD http://www.ks.uiuc.edu/Research/vmd
there is a program called VMD which is free, is supposed to do
more than you want and as far as I know runs on a pc as long as you
have OpenGL on it. But for what you want, is perfect. [editorial note:
only if the PC is running a version of the lynux kernel with Mesa
(www.redhat.com) to emulate OpenGL]
You can represent the molecules any way you want, you can render the
image, you can animate it by loading multiple pdb files or a
trajectory, you can ask the program to change any color you want for
any atom you want during the animation and you can also take a snapshot
of each frame. All these you can have set up in one script using Tcl or
do you by hand.
For a sample of the animations you can do with it check the web at the
same location.
* VMD http://www.ks.uiuc.edu/Research/vmd/
can write to various 3D file formats, like POV-Ray{2,3}, Raster3D
and VRML, as well as do trajectory animations and run in batch mode.
VMD is free and runs best on SGIs, but slower version (because of the
emulated OpenGL) are available for HPs and Linux.
The biggest problem is that no one with a strong rendering background
has worked on the code so there aren't really the hooks to tweak things
that one might expect (eg, for making all the carbons be ebony or the
surface be made of semi-transparent glass. We are open to suggestions,
and you can get the VMD source to add your own tweaks.
For a short tutorial I wrote a few months ago for making movies (with
Raster3D), see http://www.ks.uiuc.edu/Research/vmd/workshop/movie.html
(The general workshop notes, which help give an idea what VMD can do
are at http://www.ks.uiuc.edu/Research/vmd/workshop/
.)
* gOpenMol http://laaksonen.csc.fi/gopenmol/gopenmol.htmls
* Re_View
http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm
It sounds
like Re_View(2) is exactly what you want. It provides complete control
of atom colours, etc; enables multistructure XYZ files to be read in;
displays animations and even drives POV-ray without the user having to
know anything about the ray-tracing processes so that mpeg and AAplay
movies are automatically generated.
Best of all it runs under Window3.1/95/NT.
PS: Re_View contains many more features including 'active' graphs of
data, etc.
* ICMlite (see http://molsoft.com ) can do
1,2,3. It is now free for
academics. You can do something like this:
for i=1,100
read pdb "frm"+i # i.e. frm1.brk, frm2.brk etc.
display xstick
color a_//* Charge(a_//*)
color background i # this is crazy, though
delet a_
endfor
* http://www.povray.org
For those of you interested in rendering high-quality movies, I
can recommend PovRay, a highly sophisticated public domain renderer
(there is a usenet newsgroup on it out there). I know there are several
conversion filters, e.g. pdb->pov for itaround. In a Unix environment,
one would most likely use pipes, or a batch soldering individual frames
into a movie.
The new version, povray3, has many improvements, including orthographic
projection and several internal changes to increase rendering
efficiency. If you tried PovRay over a year ago and thought that it was
too slow for animation, I'd suggest trying it again. You can also use
the features of PovRay to make animations based on a single coordinate
set, e.g. rotations, pans and zooms, lighting changes, etc.
A caveat about pdb2pov-- it creates one or two large compound objects
using the constructive solid geometry (CSG) feature of PovRay; this
defeats most of the new changes for efficiency, which in general apply
divide-and-conquer approaches based on the number of objects and their
distribution in space. Removing the CSG statements (e.g. merge or
union) results in 50-fold decreases in rendering time for scenes with a
few thousand atoms. I modified the copy of pdb2pov at our local site to
avoid the use of CSG in the output .pov files. I've forwarded this
information to the author of pdb2pov, who is working on a new version
(as time allows).
Like any programming language, it takes a little time to learn how to
make the best use of PovRay. However, the documentation is available in
HTML format and is very good for a public domain program. The results
are also well worth the effort; PovRay has many pre-defined textures
(e.g. glass, stone, wood, ...) and other features that can be used to
produce journal-cover quality molecular images.
* ChemSymphony http://www.cherwell.com/chemsymphony
Animation is one of the features of ChemSymphony (URL below) which
is a publishing tool for including structures in HTML documents. This
essentially works by creating a series of frames which are rendered in
series. It recognises most file formats (XYZ, XMOL, PDB and so on) and
allows the net user to change orientation and manipulate the structure
whilst the animation is going on. A free demo is available from the
Cherwell web site.
Check Out ChemSymphony - rated top 1% Java applet by JARS
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Comments? mail me!
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