From charwel #*at*# chrs1.chem.lsu.edu Thu Jun 12 10:48:36 1997 Received: from chrs1.chem.lsu.edu for charwel - at - chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id KAA21473; Thu, 12 Jun 1997 10:29:21 -0400 (EDT) Received: by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA18084; Thu, 12 Jun 1997 09:32:46 -0500 Date: Thu, 12 Jun 1997 09:32:46 -0500 (CDT) From: Chris Harwell To: CHEMISTRY-0at0-www.ccl.net Subject: CCL animation summary (text) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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. ---------------------------------------------------------------------------- * 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 ---------------------------------------------------------------------------- Comments? mail me!