From matt@mercury.aichem.arizona.edu Wed Jul 21 04:13:10 1993 Date: Wed, 21 Jul 1993 11:13:10 -0700 (MST) From: Matthew Stahl Subject: animation To: chemistry@ccl.net Message-Id: Sorry for the delay, but here is the summary of responses to my post requesting information about animation. Thanks to everyone who responded! --------------------------------------------------------------------------- Post: Hello Netters, I am wondering how many of you have used animation as a teaching or research tool. What platforms and software are available to do this sort of thing besides Cache? If you had the ability to make an animation on a PC by stringing together coordinate files (like Macromodel or Xmol) what would you want to display? Dynamics simulations? Gaussian vibrational modes? Reaction Mechanisms? Would the ability to do this on a PC be useful? Thanks in advance. Responses will be summarized and posted if this request generates sufficient interest. --------------------------------------------------------------------------- Responses: --------------------------------------------------------------------------- From: Joe M Leonard AVS has the components needed to animate various chemical things, and several demonstration modules showing structural animation were developed 1-2 years ago. Contact Doug Smith at UToledo for additional information, although there are others that worked in this area. The version of SPARTAN currently scheduled for Xmas or so will have the ability to animate structures and mo's and the like. The prototype has been demonstrated for several months, but we were unable to get into the Version 3 release currently being beta tested. I imagine that animation can be done in Explorer as well - contact Henry Rzepa, who has done a bunch of work in this area as I recall (net traffic). Joe Leonard jle@world.std.com ------------------------------------------------------------------------- From: Dongchul Lim What I would animate is trajectories from molecular dynamics calculations, intrinsic recation coordinates and vibratinal modes from gaussian or mopac calculations, motion of solutes and solvents in statistical thermodynamics simulations, etc. I guess HyperChem for MS-Windows is capable of some of these animations (on PC). -DCL Department of Chemistry, Yale University ------------------------------------------------------------------------- From: Norbert Mueller The new version (3.5) of Ball & Stick, the molecular graphics package for Macintosh I have been developing, can create QuickTime movies from static moving structures or from a series coordinate files resulting from an MD run. Ball & Stick is availble from Cherwell Scientific Publishing 15 Auburn Place Brookline MA 02146 Tel: (617) 277 4200 Fax: (617) 739 4836 or Cherwell Scientific Publishing The Magdalen Centre Oxford Science Park Oxford OX4 4GA, UK Phone +44 (865) 784 800 Fax +44 (865) 784 801 or Cherwell Scientific Publishing c/o CHEM Research GmbH BeethovenstraBe 7b D-60325 Frankfurt 1 Tel: +49 (069) 4711114 Fax: +49 (069) 740496 A free demo should appear on info-mac and the michigan archives any tome now. Hope this helps Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at NorbertM (AMDA-Link Linz) ->FirstClass K360171@alijku11.earn \ K360171@alijku11.bitnet > will expire in 1994 K360171@alijku11.edvz.uni-linz.ac.at / ------------------------------------------------------------------------- From: SBPM Marc GINGOLD We use for research the animation in QUANTA on RS/6000. ------------------------------------------------------------------------- From: Henry Rzepa We are using animation modules developed using Explorer 2.0 to display vibrational modes, orbital transformations etc. This is done on SGI. We then convert to Quicktime format, which can be played on Mac or PC. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. ------------------------------------------------------------------------- From: Phil Bays I use an SGI Indigo with Spartan from WaveFunction, Inc. or LabVision from Tripos. With LabVision, I can do dynamics and "illustrate" the rotational barrier in Butane in a dynamic way (or any other molecule, for that matter). With Spartan, I can do normal mode calculations and display vibrational frequencies. I can also show HOMO's and LUMO's and therby illustrate reactivity, though that is not yer available in a dynamic way. I Understand that the new version of Spartan, due out the end of the month, will allow that. I also use a product put out by Falcon Software in Vt. called Organic Reaction Mechanisms and running on a Mac. It illustrates dynamically most of the standard reactions you want to look at in an organic course. This was put together using MacroMind Director, I thnink. Obviously, I am an organic chemist and teach in an undergraduate college situation. I sue all of these in my sophomore organic course. By the end of the year, thanks to an NSF ILI grant, we will have sufficient workstations that I can give students assignments on the computers, not just use them for classroom demos. Phil Bays Saint Mary's College Notre Dame, IN 46556 (219) 284-4663 pbays@saintmarys.edu bays@indigo.saintmarys.edu ------------------------------------------------------------------------- From: Barry Rowe Matt, We here at the NCSA ChemViz group use animations extensively. We use either NCSA Collage or NCSA Image to animate calculated images to show changes in molecular shape as atoms approach or move apart. We are developing curricular materials for high school Chemistry teaching. Our most useful animations are slices through the centers of (some) of the atoms in a molecule as bonds are formed. We also use graphs of the lowest energy of the total system to determine bond length (and sometimes bond angle). Our images are calculated with NCSA DISCO on a Cray. If you have any questions, please contact me. barry [] [] [] [] [] [] [] [] [] Barry E. Rowe browe@ncsa.uiuc.edu NCSA ChemViz group 240 CAB, 152 E. Springfield Ave. Champaign, IL 61820 ANY PRACTICAL APPLICATION OF PHYSICS OBVIOUSLY INVOLVES MATTER, AND IS THEREFORE CHEMISTRY. [] [] [] [] [] [] [] [] [] ------------------------------------------------------------------------- From: Richard Gillilan > > > Hello Netters, > I am wondering how many of you have used animation as a teaching > or research tool. What platforms and software are available to do this > sort of thing besides Cache? I use IBM Data Explorer. I'm about to release a suite of chemistry modules designed for molecular modeling with emphasis on animation production. I'll announce to the list when available (next couple of weeks). In practice we find that DX is quite a good tool for education (about the use of graphics). When it comes to actual simulation, something like Hyperchem or macromodel may be better. >If you had the ability to make an animation > on a PC by stringing together coordinate files (like Macromodel or Xmol) > what would you want to display? Dynamics simulations? Gaussian > vibrational modes? Reaction Mechanisms? Would the ability to do this on > a PC be useful? Most requests I get are for videos used in conference presentations, although recently one of my clients had a request for a tape to be used in a biophysics class. The subject is normal-mode vibrations of proteins (G-Actin in this case). I'd like to see more of this, but some argue, and justifyably so I think, that video is not a very good medium for education. Students have no chance for interaction or to ask questions and get more detailed explanations or to get the information at a slower pace. Interactive multimedia might be better, but then why not just let them play with the actual data using a modeling program? ------------------------------------------------------------------- stereo pair stereo pair Richard E. Gillilan H H H H Visualization Specialist \ | | \ Cornell Theory Center H--C---C--H H---C---C---H richard@tc.cornell.edu / | | / (607) 254-8757 H H H H ------------------------------------------------------------------- ------------------------------------------------------------------------- From: Williams Brian W Dear Mr. Stahl: You might want to consider contacting John Ranck at Elizabethtown College (ranck@vax.etown.edu) for possible uses of animation in teaching applications. John is heading up a group of several small college professors called the "Molecvue Corsortium" which is trying to use the advances in computational chemistry to develop and improve teaching tools. Although I have just inititated active contact with this group, they appear to be focussing on using programs such as Hyperchem , Gaussian and some commercially available animation products to further teaching goals. Perhaps you could get some ideas/insight from him, or other members of this group. Best, Brian Williams ------------------------------------------------------------------------- From: WILLSD@conrad.appstate.edu Matt: I have recently used animations in a way similar to you interests. I had a student in need of a programming problem and suggested that he write a filter program that reads a g92 freq output file and generates from it sequence of .xyz images that can be animated in xmol. I used this in my physical chemistry class to show the students what normal modes look like, and why they have the symmetry designations that they do. It was effective, but rather cosy: we do not have facilities for this in classrooms, so I had all of the students crowd in my office to look at my screen. Luckily there were only 9 students. I would be interested in hearing what sorts of responses you get, especially if those responses describe the hardware used to display animations in the classroom. Thanks, Steve Williams ----------------------------------------------------------------------- From: CHAMH@INDSVAX1.INDSTATE.EDU Matt: I am familiar with a very nice utility, KGNGRAF, which operates on the RS/6000 platform. It accepts files from GAUSSIAN, MOPAC, and HONDO and can perform animations of the normal modes, as well as provide a schematic IR (RAMAN) spectrum. MO diagrams and van der Waals surfaces (among other nice features) are also represented. KGNGRAF is written by Steve Chin (IBM/Kingston). Arthur M. Halpern Department of Chemistry Indiana State University Terre Haute, IN 47809 ------------------------------------------------------------------------- From: uchjs%earth.dnet@terra.oscs.montana.edu Sounds like a great idea. I have written an MD program that runs on a PC and displays a 3D picture in "real time". It only handles spherical force-field atoms, however. I have used it nonetheless to illustrate collision dynamics, vibrations, rotations, unimolecular dissociation and surface (and cluster) impact processes (sputtering). It should be easy to adopt to simple reaction dynamics, A + BC = AB + C. I strongly believe that simulation/animation will be a great teaching tool. For one thing, it allows for active input from the students as they can easily change parameters and see the effects. The main problem is practical - most lecture rooms do not have the equipment at hand. If market issues are your concern, you may want to take a look at a recent article (May??) on trends in the textbook market in the Wall Street Journal. Give me a message and I'll find you the date of the article. By the way, what is Cache?? Jan Sunner Chemistry Montana State University UCHJS@MTSUNIX1 ------------------------------------------------------------------------- From: Leland Wilson My guess is that PC's are more accessible to more people than are the Mac's for which Cache is designed. Now that prices are more reasonable 486's are going to be more plentiful. Any animation would be useful especially in teaching. lee wilson, Chem. Dept., La Sierra U. ------------------------------------------------------------------------- From: Louis.Grace@um.cc.umich.edu Dear Matthew, A former graduate student in my group and I (currently a graduate student) have performed quite a few GaussianTM frequency calculations. To aid in ascertaining which mode is which, we have been visualizing the molecules as they are displaced for each mode. We have been using a program called Molecular Editor to do this. The version of Molecular Editor which we have runs on a Macintosh. I do not know if there is a PC version available. (I believe it's freeware, but I'm not sure. It was written at Drexel University.) Molecular editor does perform animation by switching back and forth between two files (which contain the coordinates of the atoms at the positive and negative displacements from equilibrium). I have had to go outside our lab to do this, as our lab has only PC's! It might be desirable to have a program for the PC to do this. I thought this might interest you. Louis Grace Department of Chemistry The University of Michigan Ann Arbor, Michigan 48109