From raman@bioc01.uthscsa.edu Sat Apr 10 06:43:04 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9304101643.AA17133@bioc01.uthscsa.edu> Subject: Xpdb To: chemistry@ccl.net Date: Sat, 10 Apr 1993 11:43:04 -0500 (CDT) Since I have received numerous requests regarding the availability of Xpdb, I am including here a note on its present status: I am trying to make arrangements with the author of the program for its distribution and porting to other platforms as well. I will let you know as soon as I hear something from him. But, do write to me if you are interested in obtaining this program along with a note describing what your application is! This will inform me about the nature of the demand for a program like Xpdb. I did forget to mention in my earlier post that Xmol (MSC) has indicated that their program will automatically stop functioning (time bomb!) in May 1993, as a consequence of commericialization. I am trying to convince the author of Xpdb to provide the program free or a small licensing fee. In addition, users can provide suggestions or improvements to make the program available to a larger audience. My hope is that Xpdb will serve that purpose and will never be commercialized. . -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From HSUS@chemv2.mps.ohio-state.edu Sat Apr 10 13:00:00 1993 Date: Sat, 10 Apr 1993 18:00 EST From: HSUS@chemv2.mps.ohio-state.edu Subject: basis set for iodine To: CHEMISTRY@ccl.net Message-Id: <5277724760400124@chemv2.mps.ohio-state.edu> Dear Netters: Does anyone have iodine basis set which uses double-zeta functions for all electrons and also includes polarization and diffuse functions? If the answer is yes, would you please send it to me. Thanks. Sincerely yours, Ruth Hsu hsus@chemv2.mps.ohio-state.edu From phung@spin.chem.utah.edu Sat Apr 10 11:17:37 1993 Date: Sat, 10 Apr 1993 17:17:37 -0600 From: phung@spin.chem.utah.edu Message-Id: <9304102317.AA30730@spin.chem.utah.edu> To: CHEMISTRY@ccl.net Subject: Molecular Visualization Stuff Chemistry list readers, For those of you are interested in molecular visualization stuff, here is the resources that I found from comp.graphics. I hope you find them useful. I havn't find one for the RS6000 yet. - CGP - ============================================================================= 18. Molecular visualization stuff --------------------------------- [ Based on a list from cristy@dupont.com < Cristy > , which asked for systems for displaying Molecular Dynamics, MD for short ] Flex ---- It is a public domain package written by Michael Pique, at The Scripps Research Institute, La Jolla, CA. Flex is stored as a compressed, tar'ed archive (about 3.4MB) at perutz.scripps.edu [137.131.152.27], in pub/flex. It displays molecular models and MD trajectories. [require xview. The distribution is for Sun, DEC, and Stardent platforms]. MacMolecule ----------- (for Macintosh). I searched with Archie, and the most promising place is sumex-aim.stanford.edu (info-mac/app, and info-mac/art/qt for a demo) MD-DISPLAY ---------- Runs on SGI machines. Call Terry Lybrand (lybrand@milton.u.washington.edu). XtalView -------- It is a crystallography package that does visualize molecules and much more. It uses the XView toolkit. Call Duncan McRee landman@hal.physics.wayne.edu: ----------------------------- I am writing my own visualization code right now. I look at MD output (a specific format, easy to alter for the subroutine) on PC's. My program has hooks into GKS. If your friend has access to Phigs for X (PEX) and fortran bindings, I would be happy to share my evolving code (free of charge). Right now it can display supercells of up to 65 atoms (easy to change), and up to 100 time steps, drawing nearest neighbor bonds between 2 defining nn radii. It works acceptably fast on a 10Mhz 286. icsg0001@caesar.cs.montana.edu: ------------------------------ I did a project on Molecular Visualization for my Master's Thesis, using UNIX/X11/Motif which generates a simple point and space-filling model. KGNGRAF ------- KGNGRAF is part of MOTECC-91. Look on malena.crs4.it (156.148.7.12), in pub/motecc. motecc.info.txt Information about MOTECC-91 in plain ascii format. ---------------------------------------------------------------------------- motecc.info.troff Information about MOTECC-91 in troff format. motecc.form.troff MOTECC-91 order form in troff format. motecc.license.troff MOTECC-91 license agreement in troff format. ---------------------------------------------------------------------------- motecc.info.ps Information about MOTECC-91 in PostScript format. motecc.form.ps MOTECC-91 order form in PostScript format. motecc.license.ps MOTECC-91 license agreement in PostScript format. ditolla@itnsg1.cineca.it: ------------------------ I'm working on molecular dynamic too. A friend of mine and I have developed a program to display an MD run dynamically on Silicon Graphics. We are working to improve it, but it doesn't work under X, we are using the graphi. lib. of the Silicon Gr. because they are much faster then X. When we'll end it we'll post on the news info about where to get it with ftp. (Will be free software). XBall V2.0 ---------- Written by David Nedde. Call daven@maxine.wpi.edu. XMol ---- An X Window System program that uses OSF/Motif for the display and analysis of molecular model data. Data from several common file formats can be read and written; current formats include: Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, PDB, and MSCI's XYZ format (which has been designed for simplicity in translating to and from other formats). XMol also allows for conversion between several of these formats. Xmol is available at ftp.msc.edu. Read pub/xmol/README for further details. INSIGHT II ---------- from BIOSYM Technologies Inc. SCARECROW --------- The program has been published in J. Molecular Graphics 10 (1992) 33. The program can analyze and display CHARMM, DISCOVER, YASP and MUMOD trajectories. The program package contains also software for the generation of probe surfaces, proton affinity surfaces and molecular orbitals from an extended Huckel program. It works on Silicon Graphics machines. Contact Leif Laaksonen [ I would also suggest looking at least in SGI's Applications Directory. It contains many more packages - nfotis ] ===================