From lzj@csb0.IPC.PKU.EDU.CN Mon Mar 16 04:18:10 1998 Received: from csb0.IPC.PKU.EDU.CN for lzj@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id DAA16083; Mon, 16 Mar 1998 03:54:05 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA16349; Mon, 16 Mar 98 16:53:43 -0800 Date: Mon, 16 Mar 1998 16:53:39 -0800 (PST) From: Liu Zhijie To: Computational Chemistry List Subject: RMSD of sidechain Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am looking for some advice on RMSD calculation of protein sidechains.As we know,sidechains placement mostly is based on fixing the backbone atoms.Some papers evaluate the result with RMSD value.However I am not sure whether they calculate the value include the backbone atoms(since it will decrease the value greatly).Any suggestions will be appreciated. Sincerely yours, Elmer ********************************************************************** Chinese Name: Zhijie Liu * English Name : Elmer ********************************************************************** MOLECULAR DESIGN LABORATORY *** TEL : 8610-62751490 (LAB ) INSTITUTE OF PHYSICAL CHEMISTRY *** 8610-62752096-1082 (DORM) PEKING UNIVERSITY *** FAX : 8610-62751725 BEIJING 100871 , P.R.CHINA *** EMAIL : lzj@ipc.pku.edu.cn ********************************************************************** ADDRESS: BUILDING 46* ROOM 1082* PEKING UNIVERSITY* 100871* P.R.CHINA ********************************************************************** From mao@csb0.IPC.PKU.EDU.CN Mon Mar 16 08:18:12 1998 Received: from csb0.IPC.PKU.EDU.CN for mao@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id IAA17063; Mon, 16 Mar 1998 08:12:21 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA18992; Mon, 16 Mar 98 21:11:39 -0800 Date: Mon, 16 Mar 1998 21:11:38 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: Molecular C++ class library Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear cclers: Did someone know where is a molecular modeling c++ class library. Any reply will be apprieciated. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From prochem@biruni.erum.com.pk Mon Mar 16 09:18:11 1998 Received: from biruni.erum.com.pk for prochem@biruni.erum.com.pk by www.ccl.net (8.8.3/950822.1) id IAA17438; Mon, 16 Mar 1998 08:58:04 -0500 (EST) Received: from default by biruni.erum.com.pk (SMI-8.6/SMI-SVR4) id SAA04906; Mon, 16 Mar 1998 18:54:27 -0500 Message-ID: <350D2D14.5436@biruni.erum.com.pk> Date: Mon, 16 Mar 1998 18:45:56 +0500 From: "Zafar H. Zaidi" Reply-To: prochem@biruni.erum.com.pk Organization: HEJ Res Ins of Chemistry, Uni Karachi, Karachi, PAKISTAN. X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Neural Networks Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear ALL I would appreciate if anyone could point me to some papers and/or books on neural networks. Regards Kamran Azim Research Fellow HEJ Res Ins of Chemistry Uni of Karachi Pakistan. From beck@Ba.chem.uh.edu Mon Mar 16 11:18:20 1998 Received: from Post-Office.UH.EDU for beck@Ba.chem.uh.edu by www.ccl.net (8.8.3/950822.1) id KAA18123; Mon, 16 Mar 1998 10:58:46 -0500 (EST) Received: from Ba.Chem.UH.EDU by Post-Office.UH.EDU (PMDF V5.1-10 #18580) with SMTP id <01IUQAMV415M00074O@Post-Office.UH.EDU> for CHEMISTRY@www.ccl.net; Mon, 16 Mar 1998 09:58:47 CST Received: by Ba.Chem.UH.EDU (5.65v4.0/1.1.10.5/20Jan97-0426AM) id AA29376; Mon, 16 Mar 1998 09:58:46 -0600 Date: Mon, 16 Mar 1998 09:58:46 -0600 (CST) From: Brian Beck Subject: Digital Unix PDB viewer plugin To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Message-id: <9803161558.AA29376@Ba.Chem.UH.EDU> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Does anyone know of a PDB (or other molecular format) viewer PLUGIN for netscape that will work with Digital Unix on a DEC Alpha? I'd like to use Chime, but they don't appear to be interested in porting to Digital Unix. I can use a helper application for straight links to PDB files, but the tags trip me up, and most chem related web pages (including my own) with links to pdb files use tags. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Dept. Chemistry | | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/www/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== From rvenable@deimos.cber.nih.gov Mon Mar 16 12:18:14 1998 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA19020; Mon, 16 Mar 1998 12:08:06 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA051987922; Mon, 16 Mar 1998 12:05:22 -0500 Date: Mon, 16 Mar 1998 12:05:22 -0500 (EST) From: Rick Venable To: Liu Zhijie Cc: Computational Chemistry List Subject: Re: CCL:RMSD of sidechain In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 16 Mar 1998, Liu Zhijie wrote: > I am looking for some advice on RMSD calculation of protein > sidechains.As we know,sidechains placement mostly is based on > fixing the backbone atoms.Some papers evaluate the result with RMSD > value.However I am not sure whether they calculate the value include the > backbone atoms(since it will decrease the value greatly).Any suggestions > will be appreciated. In a well written paper, the Methods section should clearly define the atom groupings used in the analysis, such as whether or not backbone atoms are included. If several people have read the paper more than once and it still isn't clear, a polite e-mail to the cooresponding author can sometimes help answer the question. In doing your own calculations of sidechain RMSD, one thing to be careful of is the exchange of equivalent carbons. Residues where this can be a problem include PHE and TYR. Equivalent carbons can change places without affecting the interior packing or conformation.. Including these aromatic carbons in the RMSD calc can give you artificially high results; a TYR ring flip of 180 deg is exactly the same, but most software packages uniquely identify each carbon, e.g. CG1 and CG2 for the 2 carbons at the 'gamma' position. These atoms should either be excluded from the RMSD calcs, or one should check or allow for degenerate conformations. A similar situation exists for LEU and VAL, although the equivalence is inexact and an exchange of methyl positions does imply a different sidechain conformation; including CB (beta) should account for this, however. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From darrena@chem.leeds.ac.uk Mon Mar 16 13:18:13 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id MAA19171; Mon, 16 Mar 1998 12:45:38 -0500 (EST) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id RAA01245 for ; Mon, 16 Mar 1998 17:44:05 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Mar 1998 17:35:59 +0000 To: chemistry@www.ccl.net From: Darren Andrews Subject: ASROT Rotational Contour Simulation Does anybody know how to use the rotational contour simulation/fitting program ASYROT? I have the source code from the CPC archives, but there is no manual or easily understood input file. Does anybody know of an alternative program (prefferably for free) that will do similar things? Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From darrena@chem.leeds.ac.uk Mon Mar 16 15:18:14 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id OAA19837; Mon, 16 Mar 1998 14:35:59 -0500 (EST) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id TAA03157 for ; Mon, 16 Mar 1998 19:35:55 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Mar 1998 19:35:35 +0000 To: chemistry@www.ccl.net From: Darren Andrews Subject: ASROT Rotational Contour Simulation Does anybody know how to use the rotational contour simulation/fitting program ASYROT? I have the source code from the CPC archives, but there is no manual or easily understood input file. Does anybody know of an alternative program (prefferably for free) that will do similar things? Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From shenkin@still3.chem.columbia.edu Mon Mar 16 15:23:10 1998 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id OAA19840; Mon, 16 Mar 1998 14:36:00 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id OAA17612 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Mon, 16 Mar 1998 14:35:52 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id OAA07677; Mon, 16 Mar 1998 14:35:52 -0500 From: "Peter Shenkin" Message-Id: <9803161435.ZM7675@still3.chem.columbia.edu> Date: Mon, 16 Mar 1998 14:35:51 -0500 In-Reply-To: Rick Venable "CCL:RMSD of sidechain" (Mar 16, 12:05pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:RMSD of sidechain Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Mar 16, 12:05pm, Rick Venable wrote: > Subject: CCL:RMSD of sidechain > On Mon, 16 Mar 1998, Liu Zhijie wrote: > > I am looking for some advice on RMSD calculation of protein > > sidechains.As we know,sidechains placement mostly is based on > > fixing the backbone atoms.Some papers evaluate the result with RMSD > > value.However I am not sure whether they calculate the value include the > > backbone atoms(since it will decrease the value greatly).Any suggestions > > will be appreciated. > > In a well written paper, the Methods section should clearly define the > atom groupings used in the analysis, such as whether or not backbone atoms > are included. ... > > In doing your own calculations of sidechain RMSD, one thing to be careful > of is the exchange of equivalent carbons. Residues where this can be a > problem include PHE and TYR. Yup. In our paper on the subject (Proteins, 26:323-352 (1996)), we attempt a comparison with previously published work. One thing we compare is RMSD of the sidechains. We felt (and feel) strongly that the backbone atoms -- including CB -- should not be included, since the positions of these atoms are determined by phi, psi and omega, but not by the chi (sidechain) angles. Including CB and other backbone atoms in the RMSD computation artificially lowers the reported RMSD (makes the results look too good), assuming the backbone is held fixed in the computation. In our comparisons, we went to some lengths (perhaps it would be an exaggeration to claim "great lengths") to make sure we were comparing our results properly with those of other authors. There were a few situations, only, in which we could not figure out from a careful reading what the other authors had used as a convention. I believe we give this information in the Discussion part of our paper. I might add that one referee took us to task for misrepresenting one of the other authors' convention; however, we were able to show that the referee was incorrect. Incidentally, no authors, as far as I am aware, have included more than CB in this sort of work. Including CB lowers the RMS by SQRT( n / (n+1) ), where n is the number of atoms beyond CB. This factor ranges from .95 for tryptophane (n=9) to .71 for serine (n=1), assuming that no hydrogens are included explicitly. The above pertains to situations in which the backbone is held fixed and the sidechains only are varied. For modeling efforts in which the backbone is also permitted to move, it may be appropriate to include backbone atoms in RMSD; still, since backbone atoms are likely to move only a little bit (assuming a homology modeling approach, rather than a de-novo folding approach), I'd prefer to see an RMSD superposition of backbone atoms only; then, based on this superposition, seperate RMSDs for backbone atoms (including CB) and sidechains (excluding CB). In the limit of zero backbone motion, this would give 0 Angs. RMSD for the backbone and the same RMSD measure proposed above (i.e., excluding CB) for the sidechains. -P. -- ************** In memoriam, Grandpa Jones, 1913-1998, R.I.P. ************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From tj@eecs.uic.edu Mon Mar 16 19:18:15 1998 Received: from gatekeeper4.monsanto.com for tj@eecs.uic.edu by www.ccl.net (8.8.3/950822.1) id SAA21577; Mon, 16 Mar 1998 18:35:49 -0500 (EST) Received: by gatekeeper4.monsanto.com; id RAA16476; Mon, 16 Mar 1998 17:35:49 -0600 Received: from ddpc3.monsanto.com(137.35.8.13) by gatekeeper4.monsanto.com via smap (3.2) id xma016350; Mon, 16 Mar 98 17:35:27 -0600 Message-ID: <350DB77A.2B21@eecs.uic.edu> Date: Mon, 16 Mar 1998 17:36:27 -0600 From: "TJ O'Donnell" Reply-To: tj@eecs.uic.edu X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Brian Beck CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Digital Unix PDB viewer plugin References: <9803161558.AA29376@Ba.Chem.UH.EDU> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Brian Beck wrote: > > Does anyone know of a PDB (or other molecular format) viewer > PLUGIN for netscape that will work with Digital Unix on a > DEC Alpha? > > I can use a helper application for straight links to PDB > files, but the tags trip me up, and most chem > related web pages (including my own) with links to pdb files > use tags. > > -Brian I bet is tripping you up because you need to configure your web server to recognize .pdb (or whatever) files and serve them up with the appropriate mime type. If you can't reconfigure your server, you can use a cgi program to produce the "Content-type: chemical/x-pdb" mime type (or whichever mime type you want to associate with your molecular structure files). TJ O'Donnell tj@eecs.uic.edu http://www.eecs.uic.edu/~tj