From chemistry-request@server.ccl.net Tue Jul 20 02:50:31 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA31143 for ; Tue, 20 Jul 1999 02:50:31 -0400 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id CAA25085 for ; Tue, 20 Jul 1999 02:42:20 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA02813; Tue, 20 Jul 99 14:41:46 -0700 Date: Tue, 20 Jul 1999 14:41:45 -0700 (PDT) From: Arthur Wang To: CCL Subject: Where to get BABEL? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, My question might be a cliche in this list. But, where to download BABEL? Any clue will be highly appreciated. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Renxiao Wang, Ph.D _/ _/ Molecular Design Laboratory _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From chemistry-request@server.ccl.net Tue Jul 20 03:35:10 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31510 for ; Tue, 20 Jul 1999 03:35:03 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@ccl.net; Tue, 20 Jul 1999 09:26:54 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id JAA03187; Tue, 20 Jul 1999 09:26:54 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <379424BD.AC6C4AC@physik.tu-muenchen.de> Date: Tue, 20 Jul 1999 09:26:54 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: symmetries Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi altogether, I perform calculations with GAUSSIAN 94 and GAUSSIAN 98. Now I need to know the symmetries of the calculated MO's but GAUSSIAN is not able to specify the symmetries good enough. Does anybody know a program (or an internet page respectively) which helps to determine them? Another similar problem is to assign the irreducible representations to the calculated frequencies of a GAUSSIAN frequency job. Does anybody know a program which is able to do this? Thanks in advance Thomas From chemistry-request@server.ccl.net Tue Jul 20 08:00:24 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA01221 for ; Tue, 20 Jul 1999 08:00:24 -0400 Received: from minotaur.shef.ac.uk (minotaur.shef.ac.uk [143.167.2.154]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id HAA29365 for ; Tue, 20 Jul 1999 07:52:11 -0400 (EDT) From: d.turner@sheffield.ac.uk Received: from pc100182.shef.ac.uk ([143.167.100.182] helo=davets_pc) by minotaur.shef.ac.uk with smtp (Exim 3.02 #2) id 116YRR-0000bk-00 for chemistry@www.ccl.net; Tue, 20 Jul 1999 12:52:13 +0100 To: chemistry@www.ccl.net Date: Tue, 20 Jul 1999 12:52:35 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: SOMFA (sic) and COMFA - 3D_QSAR Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01a) Message-Id: Hi All As a follow-up to my previous messages I have attached a mail >from Svante Wold confirming my opinion about SOMFA; i.e., that it is CoMFA but restricted to one LV (ie PC) PLS. Any comments welcome (Original posting also attached). Dave Turner ------- Forwarded Message Follows ------- From: "nouna & svante" To: Subject: Re: QSAR: SOMFA (sic) and COMFA Date sent: Sat, 19 Jun 1999 07:12:30 +0200 Dear Dave: Finally, much thanks to your kind encouragement and reminders, I have found and read and thought about the "SOMFA" method. No doubt you are right, SOMFA is just a one component PLS model in disguise. Eqn.1 in the paper is exactly the equation for the first PLS weight vector (w1), except for a normalization factor (which does not change any of the results or the equivalence). Hence, eqn. 2 gives the score values (t1) = X w1 (again, except for a normalization factor). If you now have many "blocks" of properties, say size, polarity, lipophilicity, ..., each being paramterized by a separate "probe", the weights and scores above will be "partial", each referring to a non-orthogonal property array. Then ordinary PLS would combine these in the regression step corresponding to eq.3. Eqn. 3 looks like a different approach to finding the value of c1, but when you maximize the correlations graphically as in fig.s 5 and 6, you actually make a regression (but graphically). The fact that "SOMFA" gives better results than other methods in the comparison (table 4) just indicates that the others should have had just one component. You indeed show that Comfa with one PLS component gives identical results to "SOMFA". I don't know what you want to do with this -- I will certainly spread this among my QSAR friends. Allt he best // Sincerely // Svante Svante Wold, Chemometrics, Umea University, Sweden > > Hello > > > > Has anyone looked at SOMFA from Graham Richards group? > > (JMedChem,1999,42,573-583). > > > > It appears to me that the "new" method described is equivalent > > to extracting the first PLS latent variable (LV) and no more; ie SOMFA > > r2 = COMFA PLS LV_1 r2 (for identical descriptors- ie fields, resolution > > and other set up parameters etc). > > > > Very briefly, if PLS is summarised as: > > > > X = TP + E > > > > followed by > > > > Y = TQ + F > > > > Technically, SOMFA determines the "t" vector for the first PLS LV. > > > > If I am right then the method is surely limited since many 3D-QSAR > > models use >one LV?! > > > > Can anyone confirm (or deny) my opinion? > > > > David Turner > > > > Dr David Turner Dept of Information Studies, Sheffield University Sheffield, S10 2TN Tel. 0114 2 222 650 E-mail: D.Turner@sheffield.ac.uk Dr David Turner Dept of Information Studies, Sheffield University Sheffield, S10 2TN Tel. 0114 2 222 650 E-mail: D.Turner@sheffield.ac.uk From chemistry-request@server.ccl.net Tue Jul 20 08:06:24 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA01334 for ; Tue, 20 Jul 1999 08:06:24 -0400 Received: from fringe.vpharm.com (fringe.vpharm.com [198.114.232.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id HAA29452 for ; Tue, 20 Jul 1999 07:58:07 -0400 (EDT) Received: from portal.vpharm.com by fringe.vpharm.com via smtpd (for atlantis.ccl.net [192.148.249.4]) with SMTP; 20 Jul 1999 11:58:09 UT Received: (private information removed) Sender: pwalters@vpharm.com Message-ID: <3794643A.B7FC405C@portal.vpharm.com> Date: Tue, 20 Jul 1999 07:57:46 -0400 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 4.5 [en] (X11; U; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Arthur Wang CC: CCL Subject: Re: CCL:Where to get BABEL? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Arthur Wang wrote: > > Hi, > > My question might be a cliche in this list. But, where to download BABEL? > Any clue will be highly appreciated. Not cliche at all. The old babel host at University of Arizona died quite a while ago. Babel lives in a lot of places on the net, but the "official" distribution site is http://www.eyesopen.com/babel.html Have fun, Pat -- W. Patrick Walters, Ph.D. Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6242 FAX: (617)577-6400 -------------------------------------------------------------------- friends don't let friends write FORTRAN code From chemistry-request@server.ccl.net Tue Jul 20 08:51:28 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA01678 for ; Tue, 20 Jul 1999 08:51:28 -0400 Received: from icarus.cc.uic.edu (ICARUS.CC.UIC.EDU [128.248.121.53]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA00666 for ; Tue, 20 Jul 1999 08:43:15 -0400 (EDT) Received: from localhost (akulka1@localhost) by icarus.cc.uic.edu (8.8.8/8.8.8) with ESMTP id HAA27714; Tue, 20 Jul 1999 07:42:00 -0500 (CDT) X-Authentication-Warning: icarus.cc.uic.edu: akulka1 owned process doing -bs Date: Tue, 20 Jul 1999 07:41:56 -0500 (CDT) From: Amit Subhash Kulkarni X-Sender: akulka1@icarus.cc.uic.edu To: Arthur Wang cc: CCL Subject: Re: CCL:Where to get BABEL? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Check out www.ccl.net Cheers Amit On Tue, 20 Jul 1999, Arthur Wang wrote: > > Hi, > > My question might be a cliche in this list. But, where to download BABEL? > Any clue will be highly appreciated. > > Best wishes, > > Arthur > > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > _/ Renxiao Wang, Ph.D _/ > _/ Molecular Design Laboratory _/ > _/ Institute of Physical Chemistry, Peking University _/ > _/ Beijing 100871, P.R.China _/ > _/ _/ > _/ E-mail: arthur@ipc.pku.edu.cn _/ > _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ > _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > * * ********************************** * * * FROM: * * * * * * * * Amit S. Kulkarni * * * * * ********* * * * 903 South Ashland Ave. * ********** * Apt. No. 510 B * * * Chicago, Il 60607 * * * USA * * * * * * * ********** * Tel# 312-829-2341 * * * ********* * Email:akulka1@uic.edu * * * * * *CONCENTRATION IS ESSENCE OF LIFE* * * .....swami vivekananda* * ********************************** * ********* COLLEGE OF PHARMACY MEDICINAL CHEMISTRY DEPARTMENT MOLECULAR MODELLING LABORATORY From chemistry-request@server.ccl.net Tue Jul 20 09:46:12 1999 Received: from sos1.chem.iupui.edu ([134.68.137.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA02060 for ; Tue, 20 Jul 1999 09:46:11 -0400 Received: from localhost (dgao@localhost) by sos1.chem.iupui.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id IAA18251 for ; Tue, 20 Jul 1999 08:34:11 -0500 (EST) Date: Tue, 20 Jul 1999 08:34:11 -0500 From: Daquan Gao To: chemistry@ccl.net Subject: RE: CCL:Geometry question, send again if not solved In-Reply-To: <990720090431.21856513@ESVAX-MAIL.ES.DUPONT.COM> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Since there is some interest in the question, I will post my solution. I suppose this is the same as the original question. The original question: Given 3 points, A(a1, a2, a3), B(b1,b2,b3) and C(c1,c2, c3), find the coordinate of a fourth point (or atom) D(x,y,z) provided with the following 3 conditions: distance BD, angle ABD, angle ACD. I propose the following recipe, (1) Find distances, AD and CD based upon the angle and distance of the related triangles. (2) Using the angle and distances in triangle ABD, set up an equation: (a1-b1)(x-b1) + (a2-b2)(y-b2)+ (a3-b3)(z-b3)= AB. BD.cos(ABD). Similarly, set two other equations like this one. (3) Solve the 3 linear equations for x, y, and z. Besides, there is a more standard procedure than this, namely DISTANCE GEOMETRY method. It is not really necessary for this problem. Sincerly, Daquan Gao From chemistry-request@server.ccl.net Tue Jul 20 11:07:11 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA02750 for ; Tue, 20 Jul 1999 11:07:11 -0400 Received: from gatekeeper.es.dupont.com (gatekeeper.es.dupont.com [192.26.233.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA05445 for ; Tue, 20 Jul 1999 10:58:57 -0400 (EDT) From: fredvc@esalp1.dnet.dupont.com Received: from ns1-tmp.es.dupont.com (ns1-tmp.es.dupont.com [138.196.90.14]) by gatekeeper.es.dupont.com (8.9.3/8.9.3) with SMTP id KAA00190 for ; Tue, 20 Jul 1999 10:58:12 -0400 (EDT) Received: by ns1-tmp.es.dupont.com; id AA17671; Tue, 20 Jul 99 10:57:22 -0400 Message-Id: <9907201457.AA17671@ns1-tmp.es.dupont.com> Received: from esalp1.dnet; by esds01.dnet; Tue, 20 Jul 99 10:58:12 EDT Date: Tue, 20 Jul 99 10:58:12 EDT To: chemistry@ccl.net Cc: fredvc@esalp1.dnet.dupont.com Subject: RE: CCL: GEOMETRY QUESTION The problem outlined below was recently proposed to the list for comment: Given a fragment A-B-C, one wishes to attach a fourth atom, D, with the available information being: r(BD) <(ABD) <(CBD) how can one *uniquely* define the coordinates of D?? There is not enough information to define D uniquely. Consider the situation with the ABC fragment is constrained to the xy-plane: A / D--B \ C Unless the angles <(ABC), <(ABD), & <(CBD) sum to 360 deg., ther will be 2 solutions for the coordinates of D, differing in the algebraic sign for the z-coordinate. In order to uniquely locate D one needs one additional piece of information. Two possibilities are: out-of-plane angle (signed) for the BD bond dihedral angle A-C-B-D (signed) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Sr. Research Associate Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue Jul 20 15:40:58 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04483 for ; Tue, 20 Jul 1999 15:40:58 -0400 Received: from oncidium (ONCIDIUM.TC.CORNELL.EDU [128.84.181.31]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id PAA20578; Tue, 20 Jul 1999 15:32:43 -0400 Message-Id: <3.0.3.32.19990720153140.00a99960@tc.cornell.edu> X-Sender: cal@tc.cornell.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Tue, 20 Jul 1999 15:31:40 -0400 To: chemistry@ccl.net From: Linda Callahan Subject: October Symposium Cc: cal@tc.cornell.edu Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Could you kindly post the following symposium announcement to your list? Thank you. "Intersections of Structural Biology and Genomics" Sponsored by the Cornell Theory Center October 14-15, 1999 G10 Biotechnology Building Cornell University Ithaca, NY 14853 Registration info at http://www.tc.cornell.edu/Events/1999/Structural.Biology/ Speakers will include: Stephen Altschul National Center for Biotechnology Information Ivet Bahar Bogazici University, Turkey "Structure-based Prediction of Protein Dynamics" Stephen Bryant National Center for Biotechnology Information "Structure Prediction by Protein Threading" Ron Elber Cornell University "The Design of Efficient folding Potentials" Hunter Moseley Rutgers University Automated Analysis of Protein NMR Data: Probnosis for Structural Genomics Gene Myers Celera "A Whole Genome Assembler for Drosophila" Harold Scheraga Cornell University "Prediction of Protein Structure by Global Optimization of a Potential Energy Function" Jeffrey Skolnick Scripps Institute "Prediction of Protein Structure and Function on Genomic Scale" David States Washington University Jeffrey Thomas Parke-Davis "Genomics in Drug Discovery" Todd Yeates UCLA Linda Callahan Associate Director Cornell Theory Center cal@tc.cornell.edu