From estiu@biol.unlp.edu.ar Fri Oct 27 08:44:52 1995 Received: from biol.unlp.edu.ar for estiu@biol.unlp.edu.ar by www.ccl.net (8.6.10/950822.1) id IAA21626; Fri, 27 Oct 1995 08:33:19 -0400 Received: (from estiu@localhost) by biol.unlp.edu.ar (8.6.9/8.6.9) id JAA27098; Fri, 27 Oct 1995 09:36:51 -0300 Date: Fri, 27 Oct 1995 09:36:49 -0300 (EST) From: Estiu Guillermina To: CHEMISTRY@www.ccl.net Subject: Re: CCL:semi-empirical methods (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 27 Oct 1995 06:30:44 -0500 From: Mike Zerner To: estiu@nahuel.biol.unlp.edu.ar Subject: Re: CCL:semi-empirical methods (fwd) Hi Guillermina, INDO/S cannot be used for heats of formation. It gives energy differences between ground and excited states for a fixed geometry, much like a propagator calculation would give. There is no nuclear repulsion given here, as it does not change in the ground and excited state at a fixed geometry, as one example. INDO/1 is capable of giving heats of formation, but the energy of the reference atoms under INDO/1 must be calibrated and subtracted >from the molecular calculation. This is something I once looked at and it does work. But the only energy my ZINDO prints out is the total energy, not the heat of formation. Perhaps Hyperchem has done this, but judging from the numbers I doubt it. If this is done correctly heats of formation are usuually somewhat to low (overbound). All the best, Mike Z. --- you might wish to forward this to the appropriate people! From echamot@xnet.com Fri Oct 27 09:29:53 1995 Received: from flood.xnet.com for echamot@xnet.com by www.ccl.net (8.6.10/950822.1) id JAA22399; Fri, 27 Oct 1995 09:18:52 -0400 Received: from echamot.xnet.com by flood.xnet.com (8.7/XNet-1.4R) with SMTP id IAA16127; Fri, 27 Oct 1995 08:13:37 -0500 (CDT) Message-ID: Date: Fri, 27 Oct 95 08:16:13 EDT From: "Ernest Chamot" Subject: Re: CCL:Compressed PDB list. To: chemistry@www.ccl.net, "NOYM" Cc: "Roger" X-Mailer: VersaTerm Link v1.1.6 Dear Roger, Your observation that: > >The PDB directory currently consists of about 3800 records. However, many >of these are different versions of the same structures (for example different >mutants of the same protein or one protein with a a number of different ligands >or a lot of DNA/RNA structures). > >It would, for a number of reasons, be very valuable to have a subset of the >PDB containing representatives ("the best structure") of each unique protein, >and important conformers. > >If anybody have done a comprehensive investigation to compile such a list >or if it is already available on the net please let me now ! I'm also >interrested in any hints how to do this without manually going through every >record in the PDB. > >Of course I'll distribute a summary to the net ! > >Greetings, >Martin Norin >Pharmacia Biopharmaceuticals >Stockholm, Sweden >e-mail: martin.norin@sto.pharmacia.se > is an important one. It is also only part of the story, in that there are also inconsistent atom labeling, so that searches for a given structure won't always find all of those hits. I don't know what public domain fixes there are, but I do know that Oxford Molecular went through the PDB database, making it consistent and fixing up irregularities. They now offer it as relational database called Iditis, so you should try contacting them. Their web page is at: http://www.oxmol.co.uk/ or I you could send email to: roger@madison.polytechnique.fr Good luck. EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 echamot@xnet.com From nauss@ucmod2.che.uc.EDU Fri Oct 27 09:44:53 1995 Received: from phem3 for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.10/950822.1) id JAA22376; Fri, 27 Oct 1995 09:17:16 -0400 Received: from UCBEH.SAN.UC.EDU (SMTPUSER@UCBEH) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HWXHCH2WG095SF5P@phem3.acs.ohio-state.edu>; Fri, 27 Oct 1995 09:17:10 EDT Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-5 #7238) id <01HWXHA8LMRAHV0X3H@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Fri, 27 Oct 1995 09:15:33 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:chemistry@www.ccl.net id AA22462; Fri, 27 Oct 1995 09:16:48 -0400 Date: Fri, 27 Oct 1995 09:16:48 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:Compressed PDB list. To: chemistry@www.ccl.net Reply-to: nauss@ucmod2.che.uc.EDU Message-id: <9510271316.AA22462@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT >From: "NOYM" >It would, for a number of reasons, be very valuable to have a subset of the >PDB containing representatives ("the best structure") of each unique protein, >and important conformers. > >If anybody have done a comprehensive investigation to compile such a list >or if it is already available on the net please let me now ! I'm also >interrested in any hints how to do this without manually going through every >record in the PDB. Perhaps Laura Walsh's Annotated PDB File Listing could be useful in this regard or at least perhaps Laura could include such a listing in the next edition of her listing. She has broken down the PDB by molecule or compound. I have found this listing to be most useful for searching the PDB before the advent of PDB-Browse on the WWW. Her recommended citations for the listing are: Suggested citations for use of this file are: L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5, Diskette Appendix (1992). L. L. Walsh, "Annotated PDB File Listing", personal communication, (1994). The latest revision I have of the listing is April 1994. Does anyone know of a more up to date listing? Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC http://www.che.uc.edu/~nauss * **************************************************************************** From haney@netcom.com Fri Oct 27 10:14:57 1995 Received: from netcom11.netcom.com for haney@netcom.com by www.ccl.net (8.6.10/950822.1) id KAA23822; Fri, 27 Oct 1995 10:14:12 -0400 Received: by netcom11.netcom.com (8.6.12/Netcom) id HAA00737; Fri, 27 Oct 1995 07:11:19 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199510271411.HAA00737@netcom11.netcom.com> Subject: Re: CCL:Compressed PDB list. To: martin.norin@sto.pharmacia.se (NOYM) Date: Fri, 27 Oct 1995 07:11:19 -0700 (PDT) Cc: CHEMISTRY@www.ccl.net In-Reply-To: <4841132326101995/A23911/MEANIE> from "NOYM" at Oct 26, 95 11:13:06 pm X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1267 Martin Norin writes in part: > The PDB directory currently consists of about 3800 records. However, many > of these are different versions of the same structures (for example different > mutants of the same protein or one protein with a a number of different ligands > or a lot of DNA/RNA structures). > > It would, for a number of reasons, be very valuable to have a subset of the > PDB containing representatives ("the best structure") of each unique protein, > and important conformers. > > If anybody have done a comprehensive investigation to compile such a list > or if it is already available on the net please let me now ! I'm also > interrested in any hints how to do this without manually going through every > record in the PDB. I believe that Biosym has in the past culled the unique structures for its loop searching algorithm. You might check with Biosym to see if they provide a list of those structures. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From toukie@zui.unizh.ch Fri Oct 27 10:59:55 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/950822.1) id KAA25020; Fri, 27 Oct 1995 10:52:46 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA05476; Fri, 27 Oct 95 15:52:30 +0100 X-Nupop-Charset: Swiss Date: Fri, 27 Oct 1995 16:52:51 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <60772.toukie@zui.unizh.ch> To: chemistry@www.ccl.net, toukie@zui.unizh.ch Subject: Configns. of chiral 3o ROHs Dear Colleagues; If anyone out there is aware of a reference to the application of Horeau's or Prelog's methods or of Mosher's NMR method using MTPA in order to determine the chirality of a _tertiary_ alcohol R1 | R2 - C-OH | R3 where neither R1, R2, or R3 = H, kindly send me the exact citation as soon as possible. Thanks in advance to all responders. Sincerely, (Dr.) S. Shapiro Inst. f. orale Mikrobiol. u. allg. Immunol. Zent. f. Zahn-, Mund-, u. Kieferheilkd. der Univ. ZH Plattenstr. 11 Postfach CH-802 ZH 7 Internet: toukie@zui.unizh.ch From VARNAI@ch.bme.hu Fri Oct 27 11:59:56 1995 Received: from ns.bme.hu for VARNAI@ch.bme.hu by www.ccl.net (8.6.10/950822.1) id LAA26452; Fri, 27 Oct 1995 11:55:56 -0400 Received: from ch.bme.hu (ch.bme.hu [152.66.64.1]) by ns.bme.hu (8.6.12/8.6.12) with SMTP id QAA04068 for ; Fri, 27 Oct 1995 16:55:42 +0100 Received: from CH/TEMPQ by ch.bme.hu (Mercury 1.12); Fri, 27 Oct 95 17:06:28 +1100 Received: from TEMPQ by CH (Mercury 1.12); Fri, 27 Oct 95 17:06:04 +1100 From: "Varnai Peter" To: chemistry@www.ccl.net Date: Fri, 27 Oct 1995 17:05:56 GMT+100 Subject: Summary of sigma delocalization X-Confirm-Reading-To: "Varnai Peter" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <648068E3DB8@ch.bme.hu> Dear CCLers, I expected a bit more interest in sigma aromaticity, but anyway, here is my short summary of letters I got. My thanks to those who replied. If anyone has comments, new thoughts please contact me. Original: I am involved in a pericyclic reaction mechanism...My question is: What do YOU think about having a TS that is stabilized by sigma aromaticity? Are You aware of any references on this topic? Probably in Prof. Dewar's paper in Mol. Struct. Energ. (1988,6,1-61) there is something about this. Unfortunately, I don't have access to this paper. I hope that You share Your opinions, and I can summarize to all of You! Answers: 1, from Andreas Goeller you asked about work on sigma-aromaticity? Did you get any references? I'm working on this effect in three membered rings Y Y Y Y Y=F, OH, Cl, NH2, Br, I, CH3, H \ / \ / X=P, Si X and X charge=+1 for P; 0 for Si / \ / \ C===C C---C There is a sigma* orbital on phosphorus which interacts with the double or single bond C=C /C-C. We call this sigma*-aromaticity. I would interested to get the references you got from CCl to get more background on this topic, even if it's not exactly the same problem. Thanks in advance Bye, AHG... 2, from Vernon G. Box What is sigma aromaticity and which cyclic hydrocarbons would not have it? VB 3, from George Ford There is nothing mysterious about conjugative interactions involving sigma bonds. After all their designation as "sigma" is based purely on their local symmetry. You can find Dewar's ideas in an older, but much more accessible paper: Dewar, M. J. S., J. Am. Chem. Soc. 1984, 106, 669-682. Hope this helps, George Ford ################################################################# Peter Varnai PhD student varnai@ch.bme.hu From owner-chemistry@ccl.net Fri Oct 27 13:14:57 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA28149; Fri, 27 Oct 1995 13:07:28 -0400 Received: from chemul.uni.lodz.pl for pitsel@chemul.uni.lodz.pl by bedrock.ccl.net (8.6.10/950822.1) id NAA19379; Fri, 27 Oct 1995 13:07:15 -0400 Received: by chemul.uni.lodz.pl (5.65/25-eef) id AA09411; Fri, 27 Oct 95 18:07:44 +0200 Message-Id: <9510271607.AA09411@chemul.uni.lodz.pl> From: pitsel@chemul.uni.lodz.pl (Piotr Seliger) X-Mailer: SCO System V Mail (version 3.2) To: chemistry@ccl.net Subject: AM1 vs PM3 Date: Fri, 27 Oct 95 18:07:44 MESZ Dear Netters, Is anyone aware of any recent references concerning the comparison of AM1 vs PM3 methods resutlts for different organic compounds? Please reply to my personal e-mail address, I will post a summary to the net if I get any useful hints. Thanks for Your help! Piotr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Piotr Seliger PPP I TTT SSS EEE L Department of General P P I T S E L and Inorganic Chemistry, PPP I T SSS EE L University of Lodz, P I T S E L Narutowicza 68, P I T SSS EEE LLL 90-136 Lodz, POLAND "The right to knowledge is like E-mail: pitsel@chemul.uni.lodz.pl the right to life" (G.B.Shaw) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Thu Oct 26 19:17:42 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA11451; Thu, 26 Oct 1995 19:01:49 -0400 Received: from styx.iqm.unicamp.br for bruns@IQM.Unicamp.BR by bedrock.ccl.net (8.6.10/950822.1) id TAA13100; Thu, 26 Oct 1995 19:01:37 -0400 Received: (bruns@localhost) by styx.iqm.unicamp.br (8.6.10/IQM-ANSP1.5) id UAA00294; Thu, 26 Oct 1995 20:57:53 -0300 From: Roy Edward Bruns Posted-Date: Thu, 26 Oct 1995 20:57:53 -0300 Message-Id: <199510262357.UAA00294@styx.iqm.unicamp.br> Subject: VIII Brazilian Symposium on Theoretical Chemistry To: chemistry@ccl.net Date: Thu, 26 Oct 1995 20:57:51 -0300 (EST) VIII Brazilian Symposium on Theoretical Chemistry November 19-22, 1995 Caxambu,MG,Brazil You can use the internet to obtain copies of some or all of the 216 abstracts that have been accepted for the VIII Brazilian Symposium on Theoretical Chemistry. To see a list of the available abstracts send an e-mail to: listproc@iqm.unicamp.br with the following line (a subject is not necessary) index sbqt This file contains information about all the available abstracts. To receive a copy of this index just send another mail to listproc@iqm.unicamp.br with the command (for example) get sbqt indice.ans or get sbqt indice.autor There are two files of indices -- indice.ans which contains the file number of the abstract, title of the abstract, authors and key words and -- indice.fig which contains the file names of the figures corresponding to the respective file of the abstract. To obtain a specific abstract send an e-mail to listproc@iqm.unicamp.br with the command (for example) get sbqt020.ans The abstract files are in text format with layout and depending on the terminal used the accents on the portuguese and spanish words can be seen. The figures (postscript) are in ASCII format and are compacted. The pro- cedure to visualize the figures consists in saving the figure file and then proceeding as follows: uudecode fig020.eps.Z.uu uncompress fig020.eps.Z and later using a graphics program that permits visualization of postscript files or printing on a postscript printer. The commands uudecode and uncompress are available for several operating systems. This file is being sent to all those who have inscribed on the VIII SBQT list. If you know someone who would like to participate on this list please pass on this information to him. The interested person can simply send a mail to listproc@iqm.unicamp.br with the following line (a subject is not necessary) subscribe sbqt name Thank you for your attention. Roy E. Bruns Coordinator-Infrastructure VIII SBQT IQ,UNICAMP BRUNS@IQM.UNICAMP.BR From polowin@hyper.hyper.com Fri Oct 27 12:15:00 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/950822.1) id LAA26206; Fri, 27 Oct 1995 11:46:09 -0400 Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.9/8.6.9) with SMTP id LAA05627; Fri, 27 Oct 1995 11:55:32 -0400 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:gford@post.cis.smu.edu id AA06953; Fri, 27 Oct 95 11:55:25 -0400 Date: Fri, 27 Oct 95 11:55:25 -0400 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9510271555.AA06953@hyper.hyper.com> To: "George P. Ford" Subject: Re: CCL:ZINDO "Heats of formation" Cc: CHEMISTRY@www.ccl.net > Date: Thu, 26 Oct 95 18:06 CDT > From: "George P. Ford" > > Joel Polowin writes: > >> My calculations with HyperChem for benzoic acid gave heats of formation of >> -68.1 kcal/mol for AM1, -66.4 kcal/mol for PM3, and -3147.6 kcal/mol for >> ZINDO/1. ZINDO/S did not converge. PLEASE get the quoting levels right, especially for a matter like this! The following was by Paddy Kane, NOT by me! >>> Why are the ZINDO/1 and ZINDO/S methods giving me such apparently >>> incorrect values? > > I am not a Hyperchem user, but surely the answer is that the ZINDO data are > total energies, not heats of formation at all. I repeated the calculation -- optimized with AM1, then a ZINDO/1 single point calculation on that geometry, then the ZINDO/1-optimised structure. AM1-optimised: Total Energy = -37355.0409466 (kcal/mol) Total Energy = -59.527858396 (a.u.) Binding Energy = -1696.0933786 (kcal/mol) Isolated Atomic Energy = -35658.9475680 (kcal/mol) Electronic Energy = -151629.7883320 (kcal/mol) Core-Core Interaction = 114274.7473854 (kcal/mol) Heat of Formation = -68.1333786 (kcal/mol) Gradient = 0.0071126 (kcal/mol/Ang) ZINDO/1 single-point on that structure: Total Energy = -52247.3049941 (kcal/mol) Total Energy = -83.259717950 (a.u.) Binding Energy = -4768.6141418 (kcal/mol) Isolated Atomic Energy = -47478.6908523 (kcal/mol) Electronic Energy = -181378.3981024 (kcal/mol) Core-Core Interaction = 129131.0931083 (kcal/mol) Heat of Formation = -3140.6541418 (kcal/mol) Gradient = 49.3096263 (kcal/mol/Ang) ZINDO/1-optimised: Total Energy = -52254.2264407 (kcal/mol) Total Energy = -83.270747757 (a.u.) Binding Energy = -4775.5355884 (kcal/mol) Isolated Atomic Energy = -47478.6908523 (kcal/mol) Electronic Energy = -181134.0697328 (kcal/mol) Core-Core Interaction = 128879.8432921 (kcal/mol) Heat of Formation = -3147.5755884 (kcal/mol) Gradient = 0.0101942 (kcal/mol/Ang) Heats of formation are calculated as (binding energy) - (sum of atomic heats of formation); binding energy = (total energy) - (isolated atomic energy). Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From stoutepf@carbon.dmpc.com Fri Oct 27 13:59:58 1995 Received: from gatekeeper.es.dupont.com for stoutepf@carbon.dmpc.com by www.ccl.net (8.6.10/950822.1) id NAA28980; Fri, 27 Oct 1995 13:48:59 -0400 Received: by gatekeeper.es.dupont.com; id AA29239; Fri, 27 Oct 95 13:48:53 -0400 Received: by esds01.es.dupont.com; id AA02965; Fri, 27 Oct 95 13:48:46 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora Pro 2.1.3 for Macintosh X-Url: http://www.halcyon.com/stouten/index.html Date: Fri, 27 Oct 1995 13:50:24 -0400 To: chemistry@www.ccl.net From: stoutepf@carbon.dmpc.com (Pieter Stouten) Subject: Re: CCL:Compressed PDB list. At 8:16 95/10/27, Ernest Chamot wrote: >Oxford Molecular went through the PDB database, making it consistent >and fixing up irregularities. They now offer it as relational database >called Iditis, > I always wondered why they would use a relational database paradigm. Proteins are ordered and the information one wants to retrieve often involves stretches of residues with certain characteristics. Using a relational database, one needs to do many operations. It seems to me that a mixture of pattern matching (with additional bonus of easily allowing for a few mismatches) and relational operations would be much more efficient. Does anybody have any opinions about this? Thanks, Pieter. -- ** Note that my e-mail address has changed once again. I hope it will not ** ** happen again soon. Please use stoutepf@carbon.dmpc.com from now on. ** Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Internet: stoutepf@carbon.dmpc.com || Indiana Jones From ui22204@sunmail.lrz-muenchen.de Fri Oct 27 16:44:59 1995 Received: from cd1.lrz-muenchen.de for ui22204@sunmail.lrz-muenchen.de by www.ccl.net (8.6.10/950822.1) id QAA03327; Fri, 27 Oct 1995 16:35:55 -0400 Received: from sun2.lrz-muenchen.de by cd1.lrz-muenchen.de; Fri, 27 Oct 95 21:35:39 +0100 Received: by sun2.lrz-muenchen.de (4.1/SMI-4.1) id AA15181; Fri, 27 Oct 95 21:35:38 +0100 Date: Fri, 27 Oct 1995 21:35:38 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 Cc: chemistry@www.ccl.net Subject: Re: CCL:Compressed PDB list. In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 27 Oct 1995, Pieter Stouten wrote: > At 8:16 95/10/27, Ernest Chamot wrote: > > >Oxford Molecular went through the PDB database, making it consistent > >and fixing up irregularities. They now offer it as relational database > >called Iditis, > > > I always wondered why they would use a relational database paradigm. > Proteins are ordered and the information one wants to retrieve often > involves stretches of residues with certain characteristics. Using a > relational database, one needs to do many operations. It seems to me that a > mixture of pattern matching (with additional bonus of easily allowing for a > few mismatches) and relational operations would be much more efficient. > Does anybody have any opinions about this? I think there are at least two C++ libraries (PD) which put an OO abstraction layer upon the ugly flat ASCII pdb file structure (which, horrors! isn't even formally defined). I can look up the names and the pointers to them, if needed. Apropos OO, wouldn't a true OO dbase (such as Poet, which knows persistant C++ objects) come quite handy as a pdb object container? -- Eugene [ tail snipped for the bandwidth's sake ] From rmiller@bsm.biochemistry.ucl.ac.uk Fri Oct 27 17:15:04 1995 Received: from mail-d.bcc.ac.uk for rmiller@bsm.biochemistry.ucl.ac.uk by www.ccl.net (8.6.10/950822.1) id RAA04061; Fri, 27 Oct 1995 17:07:55 -0400 Received: from bsm.biochemistry.ucl.ac.uk (actually bsmcha1.biochem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (PP); Fri, 27 Oct 1995 14:05:31 +0000 Received: from bsmir09 (bsmir09 [128.40.46.46]) by bsm.biochemistry.ucl.ac.uk (950215.SGI.8.6.10/8.6.6) with ESMTP id OAA20263 for ; Fri, 27 Oct 1995 14:05:26 GMT Received: (rmiller@localhost) by bsmir09 (950215.SGI.8.6.10/8.6.6) id OAA03046; Fri, 27 Oct 1995 14:05:26 GMT Date: Fri, 27 Oct 1995 14:05:26 +0000 (GMT) From: Rob Miller To: chemistry@www.ccl.net Subject: Re: CCL:Compressed PDB list. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You can also get similar information from our CATH web page, where Chris Orengo and Alex Michie have developed a hierarchical numbering system for related folds and sequences. I suggest starting with http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html rob. On Thu, 26 Oct 1995, Scott Weston wrote: > Martin, > > I believe Chris Sander at EMBL has already done similar work (Hobohm & > Sander, Protein Sci., 1994, 3:522-544) which should be accessible via the > Net/Web at http://www.sander.embl-heidelberg.de. > > > Good luck, > > Scott > On Thu, 26 Oct 1995, NOYM wrote: > > > Dear Colleagues, > > > > The PDB directory currently consists of about 3800 records. However, many > > of these are different versions of the same structures (for example different > > mutants of the same protein or one protein with a a number of different ligands > > or a lot of DNA/RNA structures). > > > > It would, for a number of reasons, be very valuable to have a subset of the > > PDB containing representatives ("the best structure") of each unique protein, > > and important conformers. > > > > If anybody have done a comprehensive investigation to compile such a list > > or if it is already available on the net please let me now ! I'm also > > interrested in any hints how to do this without manually going through every > > record in the PDB. > > > > Of course I'll distribute a summary to the net ! > > > > Greetings, > > Martin Norin > > Pharmacia Biopharmaceuticals > > Stockholm, Sweden > > e-mail: martin.norin@sto.pharmacia.se > > > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: martin.norin@sto.pharmacia.se > > -- Original Sender From: Address: martin.norin@sto.pharmacia.se > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > Web: http://www.ccl.net/chemistry.html > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: mcgsw@cotton.vislab.olemiss.edu > -- Original Sender From: Address: mcgsw@cotton.vislab.olemiss.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > ----------------------------------------------------- Rob Miller, Ph.D. "...life too closely scrutinized will lead to madness or suicide." Biomolecular Structure and Modelling Unit (BSM), Department of Biochemistry and Molecular Biology, University College / Gower Street / London WC1E 6BT. United Kingdom. Tel: +44 171419 3896 Fax: +44 171380 7193 Internet: rmiller@bsm.bioc.ucl.ac.uk http://www.biochem.ucl.ac.uk/~rmiller ----------------------------------------------------- From hinsenk@ERE.UMontreal.CA Fri Oct 27 22:15:03 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/950822.1) id WAA07798; Fri, 27 Oct 1995 22:01:05 -0400 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by condor.CC.UMontreal.CA with ESMTP id VAA29658 (8.6.11/IDA-1.6); Fri, 27 Oct 1995 21:58:55 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id VAA04730; Fri, 27 Oct 1995 21:58:54 -0400 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id VAA15547; Fri, 27 Oct 1995 21:58:53 -0400 Date: Fri, 27 Oct 1995 21:58:53 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199510280158.VAA15547@cyclone.ERE.UMontreal.CA> To: ui22204@sunmail.lrz-muenchen.de CC: chemistry@www.ccl.net In-reply-to: (message from Eugene Leitl on Fri, 27 Oct 1995 21:35:38 +0100 (MET)) Subject: Re: CCL:Compressed PDB list. I think there are at least two C++ libraries (PD) which put an OO abstraction layer upon the ugly flat ASCII pdb file structure (which, I have been using pdb++ for a while, which does what it claims to do. However, that means "just" I/O - basically it provides input and output streams for C++ where each object read from the stream or written to the stream corresponds to one line in a PDB file. So it doesn't really do anything about the flat file structure, but it does handle the nasty details of handling Fortran-style fixed format files >from C++. pointers to them, if needed. Apropos OO, wouldn't a true OO dbase (such as Poet, which knows persistant C++ objects) come quite handy as a pdb object container? Certainly. But all OO data bases I know of are very proprietary and available only for a limited number of systems (and expensive, of course). Poet is a good example. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) -------------------------------------------------------------------------------