From Eugene.Leitl@lrz.uni-muenchen.de Sat Jun 7 08:47:22 1997 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.3/950822.1) id IAA22572; Sat, 7 Jun 1997 08:33:26 -0400 (EDT) Received: from sun6.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Sat, 7 Jun 97 14:33:26 +0200 Received: by sun6.lrz-muenchen.de (5.x/SMI-SVR4) id AA25260; Sat, 7 Jun 1997 14:33:23 +0200 Date: Sat, 7 Jun 1997 14:33:23 +0200 (MET DST) From: Eugene Leitl X-Sender: ui22204@sun6 To: Chris Harwell Cc: chemistry@www.ccl.net Subject: Re: CCL:animation In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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. Regards, Eugene Leitl From JonTeleV@bigfoot.com Sat Jun 7 09:47:22 1997 Received: from nessie.mcc.ac.uk for JonTeleV@bigfoot.com by www.ccl.net (8.8.3/950822.1) id JAA22643; Sat, 7 Jun 1997 09:13:26 -0400 (EDT) From: Received: from pcc13.li.man.ac.uk by nessie.mcc.ac.uk with SMTP (PP); Sat, 7 Jun 1997 14:13:13 +0100 Message-ID: <3399D08F.187D@bigfoot.com> Date: Sat, 07 Jun 1997 14:20:18 -0700 Organization: Manchester Computing X-Mailer: Mozilla 3.0 (Win16; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Enthaply of Solvation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Would it be possible to ask how the solvation enthaply of alanine dipeptide in water at 300K can be calculated. Is it possible to explain this at a level that a freshman with no (or very little) knowledge of mathematics or computers could understand ? JonTeleV@bigfoot.com From rvenable@deimos.cber.nih.gov Sat Jun 7 15:47:26 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id PAA23797; Sat, 7 Jun 1997 15:36:09 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA246191808; Sat, 7 Jun 1997 15:30:08 -0400 Date: Sat, 7 Jun 1997 15:30:08 -0400 (EDT) From: Rick Venable To: chemistry@www.ccl.net Subject: Re: CCL:animation In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 7 Jun 1997, Eugene Leitl wrote: > 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. There's also a web site at http://www.povray.org 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. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) From dalke@ks.uiuc.edu Sat Jun 7 17:47:26 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id QAA24007; Sat, 7 Jun 1997 16:54:45 -0400 (EDT) Received: from juneau.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA283796886; Sat, 7 Jun 1997 15:54:46 -0500 From: Andrew Dalke Received: by juneau.ks.uiuc.edu (940816.SGI.8.6.9) id PAA24738; Sat, 7 Jun 1997 15:54:44 -0500 Date: Sat, 7 Jun 1997 15:54:44 -0500 Message-Id: <199706072054.PAA24738@juneau.ks.uiuc.edu> To: chemistry@www.ccl.net Subject: CCL: animation Given the couple of responses to this thread, I guess it is time to plug some of my work :) The program that I helped develop, 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/ .) Andrew Dalke dalke@ks.uiuc.edu