From EWING@JCVAXA.JCU.EDU Wed Mar 3 18:30:00 1993 Date: Wed, 3 Mar 1993 23:30 EST From: "DAVID W. EWING (216) 397-4742" Subject: Molecular Modeling Seminar To: chemistry@ccl.net Message-Id: <01GVE12A88MO8Y58JG@jcvaxa> MOLECULAR MODELING IN THE DISCOVERY OF NEW DRUGS An American Chemical Society Presidential Satellite Seminar Bunts Auditorium Cleveland Clinic Foundation March 16 11:30 - 3:00 pm Refreshments (no lunch) Program: - X-Ray Crystallography in Drug Design (John J. Baldwin, Merck Research Labs, USA) - Use of Structure in the Design of HIV Protease Inhibitors (John W. Erickson, National Cancer Institute) - The Crystal Structure-Based Design of Novel Inhibitors of Thymidylate Synthase (Michael D. Varney, Agouron Pharmaceuticals, USA) PLUS: Reports from the Swiss Federal Institute of Technolgy and ICI Pharmaceuticals, UK FEE: $75 ACS members $85 public $10 students Checks payable to ACS Cleveland Section Pay at the door, but reservation required For reservations and directions contact: Dave Ewing ewing@jcvaxa.jcu.edu Jane Guzauskas (216) 943-4200 Lily Ng (216) 687-2467 From omar@malena.crs4.it Thu Mar 4 10:40:43 1993 Message-Id: <9303040840.AA20668@malena.crs4.it> To: chemistry@ccl.net Subject: Re: Molecular Visualization Date: Thu, 04 Mar 93 09:40:43 +0100 From: Omar G. Stradella Your message dated: Tue, 02 Mar 93 13:23:57 CST > To whom it may concern: > > I am looking for public-domain software for visualizing > molecules and solids. I would like each atom to be > represented by a sphere (preferably directionally > shaded), and also to have the possibility of putting > sticks between the spheres (ball-and-stick models) > when I choose. Preferably, the software should run > on SGI and IBM Risc machines with X-windows, > but if it only runs on > SGI machines that is still useful. > Thank you, > Anders Carlsson Take a look to SciAn, is a very nice (and free) scientific visualization package. It can do what you want and much more. From the README file: SciAn is a scientific visualization and animation program for Silicon Graphics and IBM RISC/Sytem 6000 workstations. It was developed at the Supercomputer Computations Research Institute at Florida State University to help meet the daily visualization needs of our scientists. SciAn is primarily intended to do 3-D visualizations of data in an interactive environment with the ability to generate animations using frame-accurate video recording devices. A user manual, on-line help, and technical notes will help you use the program. As a research institution, we have always relied upon the availability of free software to meet our needs, and we wanted to give something back to the research community in return. For this reason, we are making SciAn available at no charge. SciAn currently runs on two platforms: 1) Silicon Graphics 4D workstations 2) IBM RISC/System 6000 workstations Beginning with version 0.60, SciAn should run on all Silicon Graphics Power Series, Personal IRIS, and Indigo workstations with Z-buffer capability. It will not run on very old workstations, such as the 1000, 2000, and 3000 series. SciAn will run only on IBM RISC/System 6000 workstations that have 3-D graphics accelerators that provide GL compatibility. SciAn also requires a Z-buffer. If there is any question about whether your hardware provides this, please get in touch with your system manager or IBM sales representative. (IBM makes a bewildering variety of hardware, and I can't keep up, but the magic words are Z-buffer and 3-D GL compatibility.) On all workstations, SciAn ABSOLUTELY REQUIRES a Z-buffer. If you try to run it on a workstation that does not have a Z-buffer, you will get strange results. You can get it from: ftp.scri.fsu.edu, look into the directory pub/SciAn/release, the last version is scian0742.tar.Z. The documentation is in pub/SciAn/documentation. Omar -- **************************************************************************** * Dr. Omar G. Stradella - Omar.Stradella@crs4.it * * CRS4 - Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna * * - Centre for Advanced Studies, Research and Development in Sardinia * * -------------------------+----------------------------+----------------- * * Casella Postale 488 | Via Nazario Sauro, 10 | 39 13' 19" North * * 09100 Cagliari CA | 09123 Cagliari CA | 9 6' 17" East * * Italy | Italy | * * -------------------------+----------------------------+----------------- * * Phone: +39 70 27 96 415 FAX: +39 70 27 96 400 or +39 70 24 10 18 * **************************************************************************** From CUNDARIT@MEMSTVX1.bitnet Thu Mar 4 01:56:00 1993 Message-Id: <199303041256.AA07805@oscsunb.ccl.net> Date: Thu, 4 Mar 93 06:56 CDT From: CUNDARIT%MEMSTVX1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Subject: density functional question To: chemistry@ccl.net Hi, Our group has just started experimenting with LDF in a small way for transition metal calcs. We are trying to calculate the binding energy of H2 to Cr(CO)5, in conjunction with some work by Ted Burkey in our Dept. who has made the first exptl. determination of this quantity. Given our lack of experience with LDF we want to be sure we are not making any serious mistakes. We are using DMol at the San Diego Supercomputer Center. First question: Are LDF methods size-consistent? Second question: Does anybody have any feeling for the effect of freezing the core density in such calcs. on properties such as energetics and geometry? Third question: I have just calcd. a binding energy of -30 kcal/mol from E(Cr(CO)5(H2)) - E(Cr(CO)5) -E(H2) using the equivalent of a double-zeta- valence-plus-polarization basis set, and a FINE mesh size. Should I believe this or is it worth the expense to go to a larger basis set, finer mesh, unfrozen core? All suggestions are welcome. Tom Cundari, Asst. Prof. Dept. of Chemistry Memphis State University Memphis, TN 38152 phone:901-678-2629 fax:901-678-3447 e-mail:cundarit@memstvx1.memst.edu From tfmolinski@ucdavis.edu Thu Mar 4 05:59:54 1993 Message-Id: <9303042151.AA02268@bullwinkle.ucdavis.edu> Date: Thu, 4 Mar 1993 13:59:54 -0800 To: chemistry@ccl.net From: tfmolinski@ucdavis.edu Subject: MAC Modelling Software: Does anyone have STELLA? Hi: I'm looking for the distributor of the rate modelling program STELLA which first made its appearance in about 1987. This program allows one to set up a set of related diff. equations for, say, using a simple graphical object oriented programming. Rate models end up looking like a flow diagram and with some boundary and initial conditions, the click of a mouse would start the program and the output would be displayed as a real time evolving graph. I'm also be interested if anyone has another MAC based program that works in the same way. Ted Molinski tel: 916 752 6358 FAX: 916 752 8995 Ted Molinski tel: 916 752 6358 FAX: 916 752 8995 From MARYJO@northeastern.edu Thu Mar 4 12:08:31 1993 Date: 04 Mar 1993 17:08:31 -0500 (EST) From: MARYJO@northeastern.edu Subject: PDB subdir organization? To: chemistry@ccl.net Message-Id: <01GVF1TK4VOY9356UQ@northeastern.edu> Hello! Please help me to figure out how to pull files from PDB by anonymous FTP. I have done it by going into their fullrelease subdirectory, but then have to hunt through 10 subdirectories (named tape1 through tape10) inside /fullrelease in order to find the file i'm looking for. Does anyone know how to determine which tape (subdirectory) a given file is located in, without looking through all of them? Thanks very much, Mary Jo Ondrechen