From chemistry-request@ccl.net Tue Apr 23 10:30:33 1991 Date: Tue, 23 Apr 91 10:05:20 EDT From: Shi Yi Yue To: chemistry@ccl.net Subject: Protein Backbone Ribbon Diagram Status: R Dr. John P. Priestle has been published a paper about BIBBON for drawing stereo cartoon of protein structures. This program is on the public domain. You may get the executables and source code (Fortrain), documentation, and test data and results (papain) by contacting him to the following address: Dr. John P. Priestle K-681.3.43 Tel. (061) 696 19 65 Ciba-Geigy Ltd. CH-4002 Basel Switzerland e-mail: PRIESTLE@FMI.CH The reference is: AU John P. Priestle TI RIBBON: a stereo cartoon drawing program for proteins SO J. Appl. Cryst. 21 572-576. 1988 Hope it's helpfull. ------------------ Shi-Yi Yue Ph.D. Biotechnology Research Institute | Phone: (514) 496-6338 6100 Royalmount Avenue | Fax: (514) 496-6232 Montreal Quebec Canada H4P 2R2 | E-mail: shiyi@bri.nrc.ca From chemistry-request@ccl.net Tue Apr 23 10:41:49 1991 Date: Tue, 23 Apr 91 10:16:03 EDT From: G. Ravishanker To: shiyi@bobino.bri.nrc.ca Subject: Protein Backbone Ribbon Diagram Status: R Thanks for the info. Ravi From chemistry-request@ccl.net Tue Apr 23 12:03:27 1991 Date: Tue, 23 Apr 91 10:08:30 CDT From: Chris Parr Subject: Protein Ribbon Graphics To: Computational Chemistry List Status: R Dr. Ravishankar, another public domain package you might investigate is one by Professor Gareth Chelvanayagam called PASS; the acronym is Protein AnalysiS System. It was written in Turbo C for MS DOS machines and uses data in the Brookhaven format. The system is described in "PASS: Simple molecular graphics system for personal computers", J. Mol. Graphics (8) 207-210 (December 1990) including 5 color plates. When I requested a reprint, Prof. Chelvanayagam kindly included the program on an included diskette. However, his address is not that given in the byline of the article but rather Department of Biocomputing, European Molecular Biology Laboratory Postfach 10.2209, D-6900 Heidelberg, [West] Germany. The program will draw proteins in many representations including ribbon backbones. It requires an adapter compatible with EGA since it uses the EGA's second screen (256K versions only) for smooth animation. Happy viewing. - Chris Parr, University of Texas at Dallas P.O.Box 830688 M/S JO 3.2 Richardson, TX 75083-0688 U.S.A. Phone: 214/690-2231 BBS: 214/690-2168 (2400/8/N/1) BITNET: PARR@UTDALLAS From chemistry-request@ccl.net Tue Apr 23 13:34:58 1991 Date: Tue, 23 Apr 91 22:26:28 GMT From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) To: chemistry@ccl.net Subject: G90 problem Status: R We recently have had problems running G90 on a SGI-220 using nohup or a batch utility. This only happens if the job is submitted from sh or ksh. If the job is submitted from csh we have no problems. These jobs ran fine for many months. Anyone know what is going on ? It is very reminiscent of the VAX event flag problem. The error message is as follows: 1Entering Gaussian System, Link 0=g90 Initial command: /usr/mol/g90/l1.exe To: Communications Network for Pharmacy-School-Based Programs of Status: R Dear Oscar. I don't remember wether I've subscribed to some pharmacy list, but I'm very interested in molecular pharmacology research. I'm a undergraduated student in chemistry and my field of research is THEORETICAL STUDIES IN LOCAL ANESTHETICS, using pattern recognition, molecular mechanics and "ab-initio" MO methods. I'll graduate in Decem- ber 1991. Please, contact me at one of the following address : . Instituto de Quimica da UFRJ CT, bl. A, sl. 412 - Cid. Universitaria 21910 - Rio de Janeiro - RJ - Brasil . E-mail: IQG74001@UFRJ . Tel: (055)(021) 590-9890 (voice) (055)(021) 290-4746 (FAX) Thanks in advance. Joao O.M.A. Lins From chemistry-request@ccl.net Tue Apr 23 19:47:03 1991 Date: Tue, 23 Apr 91 19:10:46 EDT From: shenkin@avogadro.barnard.columbia.edu (Peter S. Shenkin) To: chemistry@ccl.net Subject: Corresponding States for Real Gases Status: R Does anyone know where I can look up a set of equations that give Z(Tr,Pr) -- ie, the compressibility factor as a function of reduced T and P -- for the "consensus" of real gases? I mean the set of curves including the ones illustrated in Fig. 1.8 in Moore's Physical Chemistry, 3rd Ed., and also in most other p-chem texts. I'm thinking of putting together a teaching exercise using Mathematica which will introduce functions of several variables and partial derivatives in the context of the PVT properties of real and ideal gases; obviously, it could be extended to cover fugacity as well. I think it ought to be fun to view the Z(Tr,Pr) surfaces given by the various common equations of state, as well, but these are easy to generate. I'm interested for the moment on a fit to the real-gas data. Of course it would also be nice to be able to also superimpose data for individual real gases..... but for now, my original request stands. Any pointers? -P. -- ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************** Peter S. Shenkin, Department of Chemistry, Barnard College, New York, NY 10027 (212)854-1418 shenkin@avogadro.barnard.columbia.edu shenkin@cunixc.BITNET ***"In scenic New York... where the third world is only a subway ride away."*** From chemistry-request@ccl.net Tue Apr 23 21:38:29 1991 Date: Wed, 24 Apr 91 11:14:37 +1000 From: apa@ccadfa.cc.adfa.oz.AU (Alan P Arnold) Subject: Polypeptide alpha-helix with Amber 3.0 To: chemistry@ccl.net Status: R Thanks to all those who replied to my earlier request for creating MIN coordinate files from MD trajectories. Now, another problem. I have created an 8-mer of Alanine with neutral terminii, using Amber. The starting 'conformation' created by LINK/EDIT/PARM is an extended chain. I want to get the (Ala)8 into an alpha-helix. Naively, I thought that using constraints on the H-bond distances between the ith NH and i+3'th carbonyl-O (of about 2.0A with 'energy' of 10kcal) should spring the peptide pretty close to alpha-helical. No way. Further contstraining the H-bond angles to near 180deg as well as H-bond distance constraints still doesn't work. All this 'constraining' is done in PARM. I am obviously doing something wrong here. How do I force such a peptide into an alpha-helix? A secondary question obviously arises - what is the likelihood that MIN (or any minimiser) will find the alpha-helical conformation starting from an extended chain? Thanks again. ---- Alan Arnold | Phone: +61 62 68 8080 Chem. Department,University College | ACSNET: apa@ccadfa.oz Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV