From frj@dou.dk Sun Sep 15 13:45:00 1993 Date: 15 Sep 93 11:45 +0200 From: Frank Jensen To: chemistry@ccl.net Message-Id: <901*frj@dou.dk> Subject: DG-II program and new PDB format? Hi netters, A couple of questions: ================== 1) Can anybody give me info about Tim Havels DG-II program written in C ? Is it public domain,commercial - and where can I get it ? 2) Is there anyone with information about the new PDB (Protein Data Bank) file format ? And where can I get the description ? ================== Thanks, Frank From rossi@watson.ibm.com Wed Sep 15 03:18:01 1993 Message-Id: <9309151218.AA13955@nic-support.watson.ibm.com> To: chemistry@ccl.net Subject: ACS Computers in Chemistry Division -- Call for Posters Date: Wed, 15 Sep 93 08:18:01 -0500 From: "Angelo R. Rossi (914-945-3834)" ********************************************************* * * * AMERICAN CHEMICAL SOCIETY * * * * COMPUTERS IN CHEMISTRY DIVISION * * * * CALL FOR POSTERS * * * * Spring National ACS Meeting, San Diego, California * * * * March 13-18, 1994 * * * ********************************************************* This is a notice for people to submit abstracts for the ACS Computers in Chemistry Division (COMP) General Computational Chemistry Poster Session to be held at the Spring National ACS Meeting, March 13-18, 1994 in San Diego, California. Abstracts are due on the standard printed ACS Abstract Form by October 29, 1993 . Because of programming limitations only abstracts for POSTERS in the General Computational Chemistry Session can be accepted. There will be no ORAL presentations. General Computational Chemistry; Poster Sessions - Dr. Angelo R. Rossi, IBM Research Division, T. J. Watson Research Center, Yorktown Heights, NY 10598; Tel: 914-945-3834; Fax: 914-945-2141; e-mail: rossi@watson.ibm.com From orgk2-a.sundin@macpost.lu.se Wed Sep 15 16:56:30 1993 Subject: Re: X and modems To: dave@carbon.chem.csiro.au, chemistry@ccl.net From: Anders.Sundin@orgk2.lth.se Date: Wed, 15 Sep 93 14:56:30 +0200 Message-Id: <930915.145630.936@macpost.lu.se> >I believe you simply have to implement SLIP (serial line internet protocol) on >your Iris and use SLIP on your Mac. I don't know how bad the performance would >be but would like to find out as I want to do this too. Does anyone know >whether Mac-X supports a SLIP connection? MacX does not have to know about SLIP. You only have to indicate a SLIP connection in MacTCP. There is a free (?) Macintosh SLIP from InterCon. Archie found the latest version at Host ftp.wu-wien.ac.at (137.208.3.4) Last updated 19:59 14 Sep 1993 Location: /incoming FILE -rw-r----- 351360 bytes 11:07 2 Aug 1993 InterSLIP1.0fc3.sit.bin I don't have SLIP on any UNIX computer so I have not tried it. -Anders -- Anders Sundin e-mail: Anders.Sundin@orgk2.lth.se Organic Chemistry 2 ok2aps@selund.bitnet Lund University, P.O. Box 124 voice: +46 46 104130 S-22100 Lund, Sweden fax: +46 46 108209 From J_BROWN@uvmvax.uvm.edu Wed Sep 15 04:05:00 1993 Date: Wed, 15 Sep 1993 09:05 EST From: J_BROWN@uvmvax.uvm.edu Subject: Natural Conformation of Proteins (Question) To: chemistry@ccl.net Message-Id: <01H2YZYZ7SLC000SI4@uvmvax.uvm.edu> I have been paying some attention to the discussion about the "Natural Conformation of Proteins" and the possibilities of either a global minimum or the "absolute" minimum as the most likely natural structure. I would like to add my "2 cents worth" to the discussion, even though I am no biochemist. As far as I understand: 1. Some proteins can catalyze reactions that near 100% completion. 2. Some proteins catalyze reactions that can not be performed on the bench. Question: What is the possibility that the proteins external shrubbery is folded in what appears as a local minimum but the active site, possibly buried deep in the structure, be something like a high energy transition state, held in place by the overwhelming external shrubbery? In that case, would an (entire) protein in a local or the absolute minimum be one that has no biological activity. Am I being too simple minded, a very bad habit of mine. Jay Brown From ZUEGG@orgc.tu-graz.ac.at Wed Sep 15 09:55:13 1993 Message-Id: <9309151247.AA07182@edvz.tu-graz.ac.at> To: chemistry@ccl.net From: "Johannes Zuegg" Organization: Universtity of Technology, Graz (A) Date: Wed, 15 Sep 1993 14:41:52 MEZ-1 Subject: Symmetries Hi net, I am a graduate student and I am calculating models for the enantioselectivity of enzymatic resolutions. For deriving the models I use the properties (especially three-dimensional fields of interaction energies, see CoMFA) of the both enantiomers. As symmetric properties don't improve the amount of information, I wanted to check the amount of symmetry of the investigated fields. I did it by now graphically. For calculating the symmetry of two fields my only idea was, to transform one field and than to fit (by multiple fit) it to the other field. As result I would get the RMS difference of these two fields. But, first I must use all kinds of transformations (reflecting the fields by a line or by a point, etc.. ) and secondly I would reduce the three-dimensonal information to one value (their might exist symmetric areas even with a high RMS difference). Do you know other possibilities, programs or algorithmn that can be are used for the investigation of the symmetry of three-dimensional fields? Perhaps the problem arised already in other fields of computational chemistry. Any suggestions are apprected, especially references for further information. ----------------------------------------------------------------------------------------------------------------- If it is not a public interest for the net, please answer directly to me. In any case, I will summarize the answers for the net. ----------------------------------------------------------------------------------------------------------------- Thanks in andvance, Johannes ...................................................................... Johannes Zuegg Institute of Organic Chemistry Graz Technical University Tel : ++43-316-873-8246 Stermayrgasse 16 Fax : ++43-316-81 10 57 A-8010 Graz, Austria E-Mail : Zuegg@Orgc.Tu-Graz.Ac.At ...................................................................... From damm@urz.unibas.ch Wed Sep 15 17:52:37 1993 Date: Wed, 15 Sep 1993 15:52:37 +0200 From: wolfgang damm Message-Id: <216*/S=damm/OU=urz/O=unibas/PRMD=SWITCH/ADMD=ARCOM/C=CH/@MHS> To: chemistry Subject: xwd with 24 Bit Dear Netters, I am looking for a tool that allows me to do a window dump from a "Macromodel window". The tool should therefore be able to do this with 24 bit colours. With 8 bit colours it can be done with the xwd program. On SGI platforms a tool called snapshot is available for that purpose but not for our IBM RS/6000. Thanks a lot in advance for your efforts, Wolfgang _____________________________________________________________________ Wolfgang Damm Institute for Organic Chemistry University of Basel St. Johanns-Ring 19 4054 Basel Switzerland email: damm@urz.unibas.ch From larson@caesar.iaf.uiowa.edu Wed Sep 15 03:53:16 1993 Date: Wed, 15 Sep 1993 08:53:16 -0500 (CDT) From: David Larson Subject: Re: MOPAC on SGI To: Ilya Logunov Message-Id: On Mon, 13 Sep 1993, Ilya Logunov wrote: > Could somebody tell me where I can get the version of MOPAC > running on SGI? > > > ********************************************************* > Ilya Logunov > University of Illinois at U-C > ilya@lisboa.ks.uiuc.edu > ********************************************************* > Quantum Chemistry Program Exchange (QCPE) Department of Chemistry Indiana University Bloomington, Indiana 47405 Phone: (812) 855-4784 ------------------------------------------------------------------------------- Dave Larson | Image Analysis Facility, 70 EMRB University of Iowa | Iowa City, IA 52242 larson@caesar.iaf.uiowa.edu | (319) 335-7900 ------------------------------------------------------------------------------- From shj@rlmtc.ENET.hcc.com Wed Sep 15 12:09:04 1993 From: shj@rlmtc.enet.hcc.com Message-Id: <9309151559.AA00726@gatekeeper.hcc.com> Date: Wed, 15 Sep 93 12:00:05 EDT To: mail11:;@ccl.net; (@users.lst) Subject: Biosym Polymer Project Users Meeting September 13, 1993 Greetings, Response to the first notice of the Biosym Polymer Project Users Group Meeting was quite positive. The meeting will be held on Oct. 4 and 5 at Hoechst Celanese, in Summit New Jersey. A tentative agenda is given below: Monday Oct 4 9:00 -10:30 Introduction to AVS, AVS Chemistry Viewer, Unichem, Xmol and Other Packages - Video Tape from the North Carolina Super Computer Center. 10:30-10:45 Coffee 10:45-12:00 Demonstrations AVS Chemistry Viewer and Unichem - MSI 12:00 -1:00 Lunch 1:00-3:00 Contributed Lectures 3:00-3:15 Break 3:15 - 4:30 Discussion of Issues Tues. Oct 5 9:00 - 12:00 Contributed Lectures 12:00- 1:00 Lunch 1:00-2:00 Bringing Modeling to the Bench - Discussion 2:00-3:00 Future Directions - B. Eichinger, Biosym Technologies 3:00-3:30 Coffee 3:30 Adjourn Contributed lectures include: Molecular Dynamics Simulations of Polysaccharide Fiber: an Investigation of the Polymorphic Structures of Cellulose and their Phase Transitions - B. Hardy, NIH. Experiences with the Polymer Project at Cray Research, B. Bolding, Cray Research. Simulations of Diffusion Through Membranes - D. Bassolino-Klimas, Brystol-Myers Squibb. Monte Carlo Simulations of Polymer Chains - L. Dodd, Polytechnic University. Molecular Interaction Studies - S. Jacobson, Hoechst Celanese. Please let me know if you need hotel recommendations or directions. Best Regards, Sol Jacobson (908)-522-7948 e-mail shj@rlmtc.enet.hcc.com  %%% overflow headers %%% Apparently-To: xlhuang@cbda.aprea.army.mil, dibug@comp.bioz.unibas.ch, chemistry@ccl.net, tropsha@gibbs.oit.unc.edu, bassolino@bms.com, wtwinter@suvm.syr.edu, u11867@sdsc.edu, barry@cray.com, dodd@roebling.polu.edu, bhardy@helix.nih.gov, stouch@bms.com, tan@tci001.uibk.ac.at, lief@zeno.rice.edu, perchak@kodak.com, long@crd.ge.com, mrgreen@nap.amoco.com, gew@akzo.com, rickr@ppg.scripps.edu, david@biosym.com, thpierc@rohmhaas.com, jmorei@kodak.com, maclaren@tulane.edu, dpc@uvm.edu, bendler@crd.ge.com %%% end overflow headers %%% From msjones@whale.st.usm.edu Thu Sep 16 38:02:19 1993 From: msjones@whale.st.usm.edu (Michael Sean Jones) Message-Id: <9309151746.AA18946@whale.st.usm.edu> Subject: Address Request To: CHEMISTRY@ccl.net (chemlist) Date: Wed, 15 Sep 1993 12:46:19 +22304916 (CDT) Dear all, I am searching for information on how to contact any of the authors of a journal article with the following bibliographic information published in The EMBO Journal in 1988. The 2.0A X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases. The authors were: Wolfram Bode, Richard Engh, Djordje Musil, Ulrich Thiele, Robert Huber, Andrej Karshikov(1), Joze Brzin(2), Janko Kos(2) and Vito Turk(2) Max-Plank-Institut fur Biochemie, D-8033 Martinsried, FRG and (2) Department of Biochemistry, J. Stefan Institute, Jamova 39, YU-6100 Ljubljana, Yugoslavia (1) On leave from Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria Communicated by R. Huber The information in the article is given above. If anyone knows how to contact any of the authors of the journal article, or anyone at any of the institutions listed, please let me know as soon as possible. I thought that I had lucked out by finding a gopher site at the J. Stefan Institute in Yugoslaiva. I found a name of a person who is known there as the postmaster and an address was given: E-mail address RFC822 postmaster@ijs.ac.mail.yu Whenever I send mail to this address, it is always bounced back telling me that the host is unknown. I also tried to finger that address, and I got the same message. Is there some way to find out a host address for the computer on which the gopher server is located and running. The gopher server must be running because it is still listed in the gopher list of selections. Please help. Even if it is just a far off suggestion, please let me know. Thanks, Michael Jones University of Southern Mississippi Department of Chemistry and Biochemistry Southern Station Box 5043 Hattiesburg, MS 39406-5043 msjones@wave.st.usm.edu From hcj@gull.uncc.edu Wed Sep 15 15:34:09 1993 Date: Wed, 15 Sep 93 19:34:09 -0400 From: hcj@gull.uncc.edu (Harry C. Johnson) Message-Id: <9309152334.AA00432@gull.uncc.edu> To: chemistry@ccl.net Subject: Generic PD X-windows molecule builder/viewer Dear everyone, I am looking for source code for a generic X-windows based molecule builder/viewer. It needs to be PD since I am a poor graduate student, and I also will probably need source code. I have loaded UNIX(Linux) on a couple of PC's here, complete with X, and would like some sort of builder/viewer to run locally on them. Unless there are linux binaries for such a program out there, I will have to compile it, which is why I expect I will need source code. I am aware of several such programs, not necessarily PD, for SGI machines, and a few general X-based programs such as Xmol, but these are distributed as binaries, which won't run on a linux machine. Thanks for your time! -Harry