From Steven.Creve@chem.kuleuven.ac.be Tue May 7 04:51:23 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id EAA24902; Tue, 7 May 1996 04:15:42 -0400 (EDT) Received: by hartree.quantchem.kuleuven.ac.be id AA23158 (5.67b/IDA-1.5 for Computational Chemistry List ); Tue, 7 May 1996 10:15:33 +0100 Date: Tue, 7 May 1996 10:15:33 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:magnetic properties Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know how to convert from the A,B,C parameters usually reported in LMR spectroscopy to the Aiso, A//, etc.. values ? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From Jeffrey.Gosper@brunel.ac.uk Tue May 7 05:51:23 1996 Received: from cook.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.1/950822.1) id EAA25052; Tue, 7 May 1996 04:57:42 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by cook.brunel.ac.uk with SMTP (PP); Tue, 7 May 1996 09:30:10 +0100 Date: Tue, 7 May 1996 09:29:31 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:another dumb question about molecular mechanics To: Alexandre HOCQUET cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers and Hyperchemers, Re: Alexandre Hocquet question on the molecular mechanics optimized structure of cyclohexa-1,4-diene I have had a quick look at this problem using Nemesis (COSMIC MM force field) and also found that the pseudo-boat (torsion 25 degrees) is predicted to be more stable than the flat structure by approximately 0.7 kcal/mol. However if the optimizing is started from a flat structure (modifing benzene)than this is not kinked by Nemesis. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From Steven.Creve@chem.kuleuven.ac.be Tue May 7 07:51:26 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id HAA27317; Tue, 7 May 1996 07:47:52 -0400 (EDT) Received: by hartree.quantchem.kuleuven.ac.be id AA30920 (5.67b/IDA-1.5 for Computational Chemistry List ); Tue, 7 May 1996 13:47:27 +0100 Date: Tue, 7 May 1996 13:47:27 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:hyperfine couplings Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know how to convert from the A,B,C parameters usually reported in LMR spectroscopy to the Aiso, A//, etc.. values ? Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From ldw@csb0.IPC.PKU.EDU.CN Tue May 7 09:51:26 1996 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.7.1/950822.1) id JAA28147; Tue, 7 May 1996 09:30:40 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA27225; Tue, 7 May 96 20:26:34 -0700 Date: Tue, 7 May 1996 20:26:33 -0700 (PDT) From: ldw To: Computational Chemistry List Subject: New Bioinformatics server in China Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Collages, We are pleased to announce that the first bioinformatics server in China has been setup. It is now maintained by Molecular Design Lab, Institute of Physical Chemistry, Peking University, Beijing, China. At this infant stage, it has only mirrored protein related databases, other databases of molecular biology will soon be mirrored as requested. Under the direction of Prof. Luhua Lai, all the mirror work and database interconnections are implenmented by Mr. Dawei Lin. The Home Pages were designed by Mr. Renxiao Wang and Mr. Dawei Lin. The work is supported by the Chinese National Commision of Science and Technology. At present, we are one of three official mirror sites of PDB(Protein Data Bank) including all the ftp directories and WWW browsing. We are one of five official SCOP mirror sites. We also mirrored SWISSPROT, PIR, PROSITE, BLOCKS, but only ftp services can be provided at present. The PDB and SCOP mirror sites have been crosslinked for the convenient use of local people. Also a public molecular graphics software-Rasmol is attached to the databases. Users in China and nearby coutries or areas may find this server helpful. We would like to thank all the people who give us help and valuable suggestions and specail thanks to Prof. Joel L. Sussman, Prof. Enrique Abola, Prof. Jaime Prilusky, Dr. Dave Stampf, Dr. Nancy O. Manning for the help in setting up PDB mirror site, to Dr. Steven Brenner and Prof. Tim Hubbard for the help in setting up SCOP mirror site, to Prof. Amos Bairoch for the help in setting up SwissProt mirror site. The useful URLs related to the bioinformatics server are: The first China bioinformatics server home page: http://www.ipc.pku.edu.cn/mirror/mirror.html The home page of Institute of Physical Chemistry, Peking University: http://www.ipc.pku.edu.cn/ The PDB mirror site page: http://www.ipc.pku.edu.cn/npdb/index.html The SCOP mirror site page: http://www.ipc.pku.edu.cn/scop/ The anonymous ftp server name of IPC is: ftp.ipc.pku.edu.cn Suggestions and encouragements are welcome at lai@ipc.pku.edu.cn ----------< *** Dawei LIN *** >---------------- Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 CHINA Phone: 86-10-2751490 Fax: 86-10-2751725 Email: ldw@pschnetware.pku.edu.cn ldw@ipc.pku.edu.cn URL: http://162.105.177.12/moldes/ldw/ldw.htm ------------------------------------------------ From owner-chemistry@ccl.net Tue May 7 10:51:27 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA28543; Tue, 7 May 1996 10:20:59 -0400 (EDT) Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by bedrock.ccl.net (8.7.1/950822.1) id KAA07554; Tue, 7 May 1996 10:20:59 -0400 (EDT) From: Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I4F5T5Y9E88X1NSB@phem3.acs.ohio-state.edu>; Tue, 7 May 1996 10:20:55 EDT Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 5411; Tue, 7 May 1996 10:20:23 -0400 Date: Tue, 07 May 1996 10:09:22 -0400 (EDT) Subject: Adding H-atoms?? To: chemistry@ccl.net Message-id: <01I4F5T5Y9EA8X1NSB@phem3.acs.ohio-state.edu> Organization: East Tennessee State University X-Envelope-to: chemistry@ccl.net Content-transfer-encoding: 7BIT Dear CCL'ers I need to know how to add hydrogen atoms to a large crystallographic structure that does not report the hydrogen atom positions. Programs like ALCHEMY have an "add H" option that is useful in drawing structures, but I can't find a good way to get the coordinates into ALCHEMY. For example, one can convert crystallographic xyz coordinates into ALCHEMY input with BABEL. But this conversion involves looking at the "bonding nature" of the atoms and doesn't seem to work if the hydrogen atoms are missing. Am I doing something wrong? If not, then is there a way to "fool" ALCHEMY into accepting the input coordinates so that I can use the "add H" option? Any suggestions? Regards, Dave Close. From attila@ned1.sims.nrc.ca Tue May 7 12:51:28 1996 Received: from ned1.sims.nrc.ca for attila@ned1.sims.nrc.ca by www.ccl.net (8.7.1/950822.1) id MAA00633; Tue, 7 May 1996 12:22:28 -0400 (EDT) Message-Id: <199605071622.QAA13089@ned1.sims.nrc.ca> From: Attila Berces Subject: public domain MM FORTRAN code To: chemistry@www.ccl.net Date: Tue, 7 May 1996 12:22:26 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL11 (25)] Content-Type: text I am looking for a public domain fortran code for any parametrized molecular mechanics force field. All I really need is just the energy expression itself as a function of geometrical and atom type information. Please send your answer directly to me attila@ned1.sims.nrc.ca Thank you, Attila Berces Steacie Institute for Molecular Sciences National Research Council (Canada) 100 Sussex Drive, Ottawa, ON K1A 0R6 From owner-chemistry@ccl.net Tue May 7 13:03:23 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA00749; Tue, 7 May 1996 12:35:38 -0400 (EDT) Received: from phem3 for DAVID@UCONNVM.UCONN.EDU by bedrock.ccl.net (8.7.1/950822.1) id MAA14289; Tue, 7 May 1996 12:35:37 -0400 (EDT) Received: from UCONNVM.UCONN.EDU (MAILER@UCONNVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I4FAIWP2KG8WWIGG@phem3.acs.ohio-state.edu>; Tue, 7 May 1996 12:35:29 EDT Received: from UConnVM.UConn.Edu (NJE origin DAVID@UCONNVM) by UCONNVM.UCONN.EDU (LMail V1.2a/1.8a) with BSMTP id 7056; Tue, 7 May 1996 12:34:35 -0400 Date: Tue, 07 May 1996 12:34:12 -0400 (EDT) From: Carl David Subject: Computer Assisted Testing To: chemistry@ccl.net Message-id: <960507.123433.EDT.DAVID@UConnVM.UConn.Edu> X-Envelope-to: chemistry@ccl.net X-Mailer: MailBook 95.01.000 Content-transfer-encoding: 7BIT Knowing that this is not computational chemistry per se, perhaps some readers will be interested in the following: As a service to my students I have been placing Physical Chemistry questions on the Internet in a form which allows them to access them, attempt to answer them, and have their answers graded on the spot. For the time being, this is intended to be a practice examination format. Since 1981, I have been writing and arguing that we should move to Computer Assisted Testing, where students must demonstrate unequivocal mastery of test questions, without partial credit, to pass courses, but where trivial errors could be caught in real time and students could be given the opportunity to correct those errors before being graded ("New Ways to Test Science", College Board Review, 2, 119(1981)). These WWW questions seem an appropriate forum for judging how much help and aid one could (or should), give to students while they are taking examinations, and several of the newer questions (especially the stoichiometry one in the preliminary section) have extensive help (although not context sensitive help yet) which I am asking interested persons to look at and criticize. I am in desparate need of stimulating questions, especially in quantum mechanics, spectroscopy, and statistical thermodynamics. Any suggestions would be gratefully accepted. Criticisms are welcome also. The LateX2html files, converted appropriately to Perl, may serve as a useful example of how mathematics, text, and graphics can be incorporated into Web presentations. If you want to try the server, or have your students try it, please point NetScape or Mosaic to http://mmedia.ucc.uconn.edu/~cdavid/home.html (the above has tilde cdavid, which may not mail properly, here in Storrs tildes always disappear mysteriously). Thanks Carl David david@uconnvm.uconn.edu From elewars@alchemy.chem.utoronto.ca Tue May 7 13:51:29 1996 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.7.1/950822.1) id MAA00850; Tue, 7 May 1996 12:56:14 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id MAA23261 for chemistry@www.ccl.net; Tue, 7 May 1996 12:56:07 -0400 (EDT) Date: Tue, 7 May 1996 12:56:07 -0400 (EDT) From: "E. Lewars" Message-Id: <199605071656.MAA23261@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SHAPE OF CYCLOHEXATRIENE: MY CALCS 1996 May 7 Hello, There has been a discussion of the conformation of 1,3-cyclohexadiene as calculated by MM and AM1. I got these results, using Spartan: MM jobs: 1 C2 (nonplanar ring) input from the builder, opt with MM3-->C2, 9.12 kcal/mol 2 Cs (planar ring) input from the builder, opt with MM3-->C2v, 10.38 kcal/mol AM1 jobs: 3 C2 input from MM3, opt with AM1--> C2, 17.49 kcal/mol, no imaginary freqs 4 C2v (planar ring) input from MM3, opt with AM1--> C2v, 17.64 kcal/mol, 1 imag. freq, 74i cm-1 ("-74" cm-1) Now, an MM energy cannot be compared with an AM1 energy, since they refer to different things, but within each class of computation the C2 (nonplanar ring) geometry has the lower energy, and the AM1 C2 geom is a relative minimum on the potential energy surface, since it has no imaginary frequencies. The "small" value of the imaginary freq of the AM1 C2v structure shows that this AM1 transition state is "flat" (not steeply curved along the reaction coordinate), as might have been suspected from the very small activation energy, and animating the vibration reveals that the planar C2v molecule wants to twist to the C2 geometry. This little exercise shows (1) the importance of the _input_ geom; an MM job can throw an input structure into a higher sym, but a semiempirical or ab initio calc will keep the input symmetry (2) the importance of doing a freq job on an optimized structure, to see if it is a relative minimum or some kind of saddle point (e.g. a transition state=1st-order saddle point) ON THAT PARTICULAR PES, which is not necessarily the _true_ PES. Most MM programs do not yet do freq calcs, altho' I think the latest version of MM3 does. Does any one know what _experiment_ tells us about the shape of 1,3-hexadiene? E. Lewars Chemistry Dept Trent U, Ontario, CANADA From DAVID@UCONNVM.UCONN.EDU Tue May 7 13:59:52 1996 Received: from phem3 for DAVID@UCONNVM.UCONN.EDU by www.ccl.net (8.7.1/950822.1) id NAA01397; Tue, 7 May 1996 13:14:44 -0400 (EDT) Received: from UCONNVM.UCONN.EDU (MAILER@UCONNVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I4FBVINXOG8X1N70@phem3.acs.ohio-state.edu>; Tue, 7 May 1996 13:14:36 EDT Received: from UConnVM.UConn.Edu (NJE origin DAVID@UCONNVM) by UCONNVM.UCONN.EDU (LMail V1.2a/1.8a) with BSMTP id 9878; Tue, 7 May 1996 13:13:50 -0400 Date: Tue, 07 May 1996 13:13:26 -0400 (EDT) From: Carl David Subject: Computer Assisted Testing To: chemistry@www.ccl.net Message-id: <960507.131346.EDT.DAVID@UConnVM.UConn.Edu> X-Envelope-to: chemistry@www.ccl.net X-Mailer: MailBook 95.01.000 Content-transfer-encoding: 7BIT Knowing that this is not computational chemistry per se, perhaps some readers will be interested in the following: As a service to my students I have been placing Physical Chemistry questions on the Internet in a form which allows them to access them, attempt to answer them, and have their answers graded on the spot. For the time being, this is intended to be a practice examination format. Since 1981, I have been writing and arguing that we should move to Computer Assisted Testing, where students must demonstrate unequivocal mastery of test questions, without partial credit, to pass courses, but where trivial errors could be caught in real time and students could be given the opportunity to correct those errors before being graded ("New Ways to Test Science", College Board Review, 2, 119(1981)). These WWW questions seem an appropriate forum for judging how much help and aid one could (or should), give to students while they are taking examinations, and several of the newer questions (especially the stoichiometry one in the preliminary section) have extensive help (although not context sensitive help yet) which I am asking interested persons to look at and criticize. I am in desparate need of stimulating questions, especially in quantum mechanics, spectroscopy, and statistical thermodynamics. Any suggestions would be gratefully accepted. Criticisms are welcome also. The LateX2html files, converted appropriately to Perl, may serve as a useful example of how mathematics, text, and graphics can be incorporated into Web presentations. If you want to try the server, or have your students try it, please point NetScape or Mosaic to http://mmedia.ucc.uconn.edu/~cdavid/home.html (the above has tilde cdavid, which may not mail properly, here in Storrs tildes always disappear mysteriously). Thanks Carl David david@uconnvm.uconn.edu From bthomas@data.procept.com Tue May 7 15:51:30 1996 Received: from nic.near.net for bthomas@data.procept.com by www.ccl.net (8.7.1/950822.1) id PAA02844; Tue, 7 May 1996 15:39:30 -0400 (EDT) Received: from iris.procept.com by nic.near.net id aa05714; 7 May 96 15:24 EDT Received: from data.procept.com by iris.procept.com via ESMTP (940816.SGI.8.6.9/930416.SGI) for <@iris.procept.com:chemistry@www.ccl.net> id PAA13592; Tue, 7 May 1996 15:40:01 -0700 Received: by data.procept.com (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id PAA07203; Tue, 7 May 1996 15:40:00 -0700 From: Bert Thomas Message-Id: <9605071540.ZM7201@data.procept.com> Date: Tue, 7 May 1996 15:40:00 -0700 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: Cyclohexadienes Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I haven't followed the whole discourse on MM and AM1 calcs on 1,3-cyclohexadiene, so I will be brief. Microwave and electron diffraction studies on 1,3-cyclohexadiene are available. The structure has C2 symmetry and is well represented at the RHF/6-31G(d) level. While in the Houk group, I and others looked at the electrocyclic reactions of substituted 1,3-cyclohexadienes and at all levels of theory employed (including AM1) these structures were staggered about the sp3-sp3 single bond. The microwave and electron diffraction references are: Oberhammer, H. ... JACS 1969, 91, 10 Dallinga, G. ... J. Mol. Struc. 1968, 1, 11 Traetteberg, M. Acta. Chem. Scand. 1968, 22, 2305 Butcher, S. S. J. Chem. Phys. 1965, 42, 1830 I hope this helps. Bert -- _________________________________________________________ | | | Bert E. Thomas IV, Ph.D. bthomas@iris.procept.com | | Procept, Inc. (617)491-1100 ext 3040 | | Cambridge, MA 02139 | |_________________________________________________________| From owner-chemistry@ccl.net Tue May 7 16:01:32 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id PAA02741; Tue, 7 May 1996 15:20:10 -0400 (EDT) Received: from po6.andrew.cmu.edu for mm6n+@andrew.cmu.edu by bedrock.ccl.net (8.7.1/950822.1) id PAA17578; Tue, 7 May 1996 15:20:07 -0400 (EDT) Received: (from postman@localhost) by po6.andrew.cmu.edu (8.7.5/8.7.3) id PAA03510 for chemistry@ccl.net; Tue, 7 May 1996 15:19:38 -0400 Received: via switchmail; Tue, 7 May 1996 15:19:33 -0400 (EDT) Received: from unix13.andrew.cmu.edu via qmail ID ; Tue, 7 May 1996 15:18:39 -0400 (EDT) Received: from unix13.andrew.cmu.edu via qmail ID ; Tue, 7 May 1996 15:18:37 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix13.andrew.cmu.edu.sun4c.411 via MS.5.6.unix13.andrew.cmu.edu.sun4c_411; Tue, 7 May 1996 15:18:36 -0400 (EDT) Message-ID: Date: Tue, 7 May 1996 15:18:36 -0400 (EDT) From: Marcella Madrid To: chemistry@ccl.net Subject: CCL: --Sequence Analysis workshops offered at the PSC NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOPS FOR BIOMEDICAL RESEARCHERS PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu The following two Sequence Analysis workshops will be offered this summer: *********NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: June 9-14.************** Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are: Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information: A limited number of grants to cover travel and/or hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Complimentary breakfast and lunches will be provided. APPLICATION DEADLINE: May 17, 1996. *****ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: August 25-28.****** Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Leaders are: Dr Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information : Hotel accommodations during the workshop for researchers affiliated with U.S. academic institutions will be paid by our NIH grant. Complimentary breakfast and lunches will also be provided. There is NO REGISTRATION FEE for this workshop. All other costs incurred in attending (travel, other meals, etc.) are the responsibility of the individual participant. APPLICATION DEADLINE: July 10, 1996. ********** PITTSBURGH SUPERCOMPUTING CENTER WORKSHOPS FOR BIOMEDICAL RESEARCHERS APPLICATION Workshop I am interested in attending:_______________________________________ Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:_________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From JOHNSON_DOUGLAS_W@Lilly.com Tue May 7 16:51:30 1996 Received: from Lilly.com for JOHNSON_DOUGLAS_W@Lilly.com by www.ccl.net (8.7.1/950822.1) id QAA03228; Tue, 7 May 1996 16:48:01 -0400 (EDT) Received: from mr.lilly.com by INET.D48.LILLY.COM (PMDF V5.0-4 #15017) id <01I4FH5SWJPC0011MJ@INET.D48.LILLY.COM> for CHEMISTRY@www.ccl.net; Tue, 07 May 1996 15:45:51 -0500 (EST) Received: with PMDF-MR; Tue, 07 May 1996 20:45:14 +0000 (GMT) MR-Received: by mta MCVAX0.MUAS; Relayed; Tue, 07 May 1996 20:45:14 +0000 MR-Received: by mta MCVAX4; Relayed; Tue, 07 May 1996 20:45:13 +0000 MR-Received: by mta MCDEV1; Relayed; Tue, 07 May 1996 20:45:15 +0000 Disclose-recipients: prohibited Date: Tue, 07 May 1996 20:45:14 +0000 (GMT) From: "Doug Johnson, MC625, 6-1467" Subject: position available To: CHEMISTRY@www.ccl.net Cc: "/R=AM/U=RX23376/FFN=JOHNSON, DOUG/"@mr.lilly.com Message-id: <1314451507051996/A95442/MCVAX4/11A53BED0000*@MHS> Autoforwarded: false MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Importance: normal Priority: normal Sensitivity: Company-Confidential UA-content-id: 11A53BED0000 X400-MTS-identifier: [;1314451507051996/A95442/MCVAX4] Hop-count: 2 POSTDOCTORAL POSITION In Computational Chemistry Lilly Research Laboratories, has a position available for a Postdoctoral Fellow in computational chemistry to develop and to apply computational methods to combinatorial chemistry. The appointment will be for a period of one to two years. Candidates for this position should have a Ph.D. with a strong research background in computational chemistry or physical chemistry. Candidates must be computer fluent in numerous programming languages and workstation environments, and have good interaction skills. Candidates would be expected to functions in a multidisciplinary group composed of medicinal chemist, computational chemist, computer scientist, and statisticians. Lilly Research Laboratories provides a stimulating environment for study and state of the art science. Our computational facilities consist of several VAX computers, a central research cluster of VAX computers and a Cray J916 supercomputer. We have SGI workstations in our laboratories and have available for our use a wide variety of modeling and crystallographic software. Lilly Research Laboratories are a subsidiary of Eli Lilly and Company located in Indianapolis Indiana USA. Eli Lilly and Company is an equal opportunity employer. For further information, applicants may send a resume with references to: Dr. Joerg Pfeifer Attention: JHW Eli Lilly and Company Lilly Corporate Center Indianapolis, IN 46285-0403 Phone: 1-800-428-4592 Fax: (317)-277-9721 From owner-chemistry@ccl.net Tue May 7 17:51:30 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA03307; Tue, 7 May 1996 16:58:16 -0400 (EDT) Received: from po6.andrew.cmu.edu for mm6n+@andrew.cmu.edu by bedrock.ccl.net (8.7.1/950822.1) id QAA18879; Tue, 7 May 1996 16:57:28 -0400 (EDT) Received: (from postman@localhost) by po6.andrew.cmu.edu (8.7.5/8.7.3) id QAA04936 for chemistry@ccl.net; Tue, 7 May 1996 16:57:22 -0400 Received: via switchmail; Tue, 7 May 1996 16:57:21 -0400 (EDT) Received: from unix13.andrew.cmu.edu via qmail ID ; Tue, 7 May 1996 16:56:26 -0400 (EDT) Received: from unix13.andrew.cmu.edu via qmail ID ; Tue, 7 May 1996 16:56:23 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix13.andrew.cmu.edu.sun4c.411 via MS.5.6.unix13.andrew.cmu.edu.sun4c_411; Tue, 7 May 1996 16:56:23 -0400 (EDT) Message-ID: Date: Tue, 7 May 1996 16:56:23 -0400 (EDT) From: Marcella Madrid To: chemistry@ccl.net Subject: CCL:sequence analysis workshops offered at the PSC NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOPS FOR BIOMEDICAL RESEARCHERS PITTSBURGH SUPERCOMPUTING CENTER Biomedical Workshops offered by the Pittsburgh Supercomputing Center typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data.Attendance is limited to 20 participants to allow one-on-one instructionand encourage scientific interactions and discussions.Researchers nationwide are invited to apply. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu The following two Sequence Analysis workshops will be offered this summer: *********NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: June 9-14.************** Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are: Dr. Gary Churchill, Cornell University; Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information: A limited number of grants to cover travel and/or hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Complimentary breakfast and lunches will be provided. APPLICATION DEADLINE: May 17, 1996. *****ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS: August 25-28.****** Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. Leaders are: Dr Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. Financial Information : Hotel accommodations during the workshop for researchers affiliated with U.S. academic institutions will be paid by our NIH grant. Complimentary breakfast and lunches will also be provided. There is NO REGISTRATION FEE for this workshop. All other costs incurred in attending (travel, other meals, etc.) are the responsibility of the individual participant. APPLICATION DEADLINE: July 10, 1996. ********** PITTSBURGH SUPERCOMPUTING CENTER WORKSHOPS FOR BIOMEDICAL RESEARCHERS APPLICATION Workshop I am interested in attending:_______________________________________ Name: ______________________________________________________________ Affiliation: ______________________________________________________________ Address: ______________________________________________________________ (Business) ______________________________________________________________ ______________________________________________________________ (Home) ______________________________________________________________ Telephone: ____________________________ ____________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:_________________ Electronic Mail Address:_____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:______________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From fgonzale@lauca.usach.cl Tue May 7 21:51:31 1996 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.7.1/950822.1) id VAA05265; Tue, 7 May 1996 21:34:23 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id WAA26996 for ; Thu, 7 May 1992 22:36:54 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id VAA01383 for chemistry@www.ccl.net; Tue, 7 May 1996 21:37:05 -0400 From: Fdo Danilo Gonzalez Nilo Message-Id: <199605080137.VAA01383@lauca.usach.cl> Subject: MIRRORS for Chile To: chemistry@www.ccl.net Date: Tue, 7 May 96 21:37:05 AST Hi all!!! I am trying to set up an Web server, here in Chile. We have some difficulties for getting conections probably due to the distance. With the aim of having a quicker information access, I am asking you the following favor: Could you please give me an address for down some MIRRORs in the field of chemistry, biochemistry and computational chemistry?... and put it in my server... ;-) Thanks a lot!!!! Fernando Danilo Gonzalez N. University of Santiago of Chile Faculty of Chemistry and Biology Casilla 307, Santiago-2, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quantum.usach.cl URL : http://quantum.usach.cl/~danilo *************************************************************************x From owner-chemistry@ccl.net Tue May 7 22:00:39 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id VAA05283; Tue, 7 May 1996 21:36:09 -0400 (EDT) Received: from camsoft.com for jsb2@camsoft.com by bedrock.ccl.net (8.7.1/950822.1) id VAA20668; Tue, 7 May 1996 21:36:07 -0400 (EDT) From: Date: Tue, 7 May 96 21:36:02 EDT Received: by camsoft.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA22903; Tue, 7 May 96 21:36:02 EDT Message-Id: <9605080136.AA22903@camsoft.com> To: R29CLOSE@ETSU.EAST-TENN-ST.EDU, chemistry@ccl.net Subject: Re: CCL:Adding H-atoms?? > I need to know how to add hydrogen atoms to a large crystallographic >structure that does not report the hydrogen atom positions. > Programs like ALCHEMY have an "add H" option that is useful in >drawing structures, but I can't find a good way to get the coordinates >into ALCHEMY. > For example, one can convert crystallographic xyz coordinates into >ALCHEMY input with BABEL. But this conversion involves looking at >the "bonding nature" of the atoms and doesn't seem to work if the >hydrogen atoms are missing. This is a deficiency of Babel, not Alchemy. > Am I doing something wrong? If not, then is there a way to "fool" >ALCHEMY into accepting the input coordinates so that I can use the >"add H" option? I would look for a way to import the coordinates into Alchemy without using Babel as an intermediary. That sort of approach would definitely work with Chem3D; I have to assume the same sort of thing would would for Alchemy. If all you want is to see the hydrogens there, you could even use the freely-available Chem3D Net, which is capable of adding the hydrogens (but not of saving the modified files). Information about Chem3D and Chem3D Net is available from http://www.camsoft.com Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From Y0H8797@ACS.TAMU.EDU Tue May 7 22:51:35 1996 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.7.1/950822.1) id WAA06197; Tue, 7 May 1996 22:07:53 -0400 (EDT) Date: Tue, 7 May 1996 21:07:24 -0500 (CDT) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <960507210724.208469b8@ACS.TAMU.EDU> Subject: Drawing program to generate Z-matrix Does anybody know a drawing program we can use to generate the Z-matrix for DOS or Windows? I know CAChe Editor is very good but it's for Mac. (CAChe Editor combines with CAChe MOPAC can generate Z-matrix but Editor alone can't). It's better to be a freeware or shareware. Thank you for any response. Yong