From chemistry-request@www.ccl.net Thu Apr 8 09:06:55 1999 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA12245 Thu, 8 Apr 1999 09:06:55 -0400 (EDT) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.1/8.9.1) with ESMTP id JAA27303; Thu, 8 Apr 1999 09:06:17 -0400 (EDT) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id IAA03034; Thu, 8 Apr 1999 08:56:08 -0400 (EDT) Date: Thu, 8 Apr 1999 08:56:08 -0400 (EDT) From: Steve Heller To: ACSMEDI@LISTS.WAYNE.EDU, amber@cgl.ucsf.edu, APPLSPEC@uga.cc.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.uwf.edu, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU, isisforum-l@mdli.com, ISOGEOCHEM@LIST.UVM.EDU, listproc@msi.com, listserver@ic.ac.uk Subject: ChemInt'99 - Abstract Submission Deadline extended Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This note is to announce that final abstract submission date for poster talks at ChemInt'99 (www.chemint.org) has been extended to June 1, 1999. The web Abstract Submission form for ChemInt'99 is now operational for the Chemistry and the Internet (ChemInt'99) meeting. A number of abstracts have been submitted and those which have been accepted have been posted on the ChemInt'99 web site. ChemInt'99 is being held in at Georgetown University in Washington DC on September 25-27, 1999. The program of invited speakers and panel members of the 3 panel sessions is available on the meeting web site - www.chemint.org You are urged to look at the program and to consider submitting a poster paper to the meeting. A number of poster papers will be selected for oral presentation at the meeting. The main lecturers for the meeting will be: Alan Arnold, University College (UNSW) Steven Bachrach, Northern Illinois University Robert Bovenschulte, ACS Stephen Boyer, IBM Karl Harrison, Oxford University Clemens Jochum, Deutsche Bank Gary Mallard, NIST Tom Pierce, Rohm & Haas Jerome Reichman, Vanderbilt Achim Zielesny, Bayer AG Steven S. Zumdahl, University of Illinois at Urbana-Champaign The (current) corporate sponsors for the meeting are: ChemWeb and the Internet Journal of Chemistry Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry International Union of Pure and Applied Chemistry (IUPAC) (pending) Japan Association for International Chemical Information (JAICI) Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC) Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: chem@feldmann.nist.gov From chemistry-request@www.ccl.net Thu Apr 8 09:43:48 1999 Received: from unet.univie.ac.at (unet.univie.ac.at [131.130.230.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA12488 Thu, 8 Apr 1999 09:43:42 -0400 (EDT) Received: from brain (unet3-250.univie.ac.at [131.130.232.250]) by unet.univie.ac.at (8.8.8/8.8.7) with SMTP id PAA44108; Thu, 8 Apr 1999 15:39:05 +0200 Message-ID: <000001be81c4$eacc8e40$0100a8c0@brain> From: "Alexander Klinsky" To: "Serge Pissarev" , "Computational Chemistry List" Subject: Re: CCL:MOLDEN wanted under Win32... Date: Thu, 8 Apr 1999 15:23:58 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.0810.800 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800 Dear Serge Pissarev ! I am the one who ported the current Molden to the Windows platform. Please take a look at the official molden homepage at http://www.caos.kun.nl/~schaft/molden/molden.html from Gijs Shaftenaar. There you will find a link to "Currently tested platforms" -> "Windows 95/NT". It explains in detail where to download the binaries and run molden on the W95/98/NT platform. If you have any problems please do not hesitate to contact me. Sincerely , Alex ----------------------------------------------------------------- Alexander Klinsky Department of Applied Theoretical Biochemistry Insitute of Theoretical Chemistry University of Vienna, Austria ----------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Apr 8 11:12:28 1999 Received: from host23.lctn.u-nancy.fr (host23.lctn.u-nancy.fr [192.54.210.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13231 Thu, 8 Apr 1999 11:12:27 -0400 (EDT) From: assfeld@host23.lctn.u-nancy.fr Received: (from assfeld@localhost) by host23.lctn.u-nancy.fr (AIX4.3/UCB 8.8.8/8.7) id RAA29272; Thu, 8 Apr 1999 17:10:48 +0200 Date: Thu, 8 Apr 1999 17:10:48 +0200 Message-Id: <199904081510.RAA29272@host23.lctn.u-nancy.fr> To: rassolov@chem.nwu.edu Subject: Canonical orthogonalization Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: Bb1GeKQN3IIXRKm3b79otA== you wrote : > Does anyone know the efficient algorithm/subroutine for calculating the > basis in the orthogonal subspace? Or, more precisely: > Given N M-dimensional vectors, how to find (M-N) M-dimensional > orthonormal vectors, each of them being orthogonal to the each of the N > original vectors. > > This seems to be a very universal problem, yet I couldn't find anything in > LAPACK/NETLIB/Numerical Recipies. > > Any help will be very much appreciated > >_______ > > Vitaly Rassolov rassolov@chem.nwu.edu > Chemistry Department tel. (847) 491-3423 > Northwestern University fax (847) 491-7713 Hello, have a look at paper : X. Assfeld, and J.-L. Rivail, CHem. Phys. Lett. 263 (1996) 100. you will find what you are looking for. C.U. ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr From chemistry-request@www.ccl.net Thu Apr 8 11:49:43 1999 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13502 Thu, 8 Apr 1999 11:49:42 -0400 (EDT) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id RAA00648; Thu, 8 Apr 1999 17:50:05 +0200 Date: Thu, 8 Apr 1999 17:50:05 +0200 Message-Id: <199904081550.RAA00648@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: rassolov@chem.nwu.edu CC: chemistry@www.ccl.net In-reply-to: (message from Vitaly Rassolov on Wed, 7 Apr 1999 15:48:47 -0500 (CDT)) Subject: Re: CCL:lin.alg.? (basis set in the orthog. subspace) References: > Does anyone know the efficient algorithm/subroutine for calculating the > basis in the orthogonal subspace? Or, more precisely: > Given N M-dimensional vectors, how to find (M-N) M-dimensional > orthonormal vectors, each of them being orthogonal to the each of the N > original vectors. Such a set of vectors can be obtained as a "side effect" of singular value decomposition (SVD). I use the SVD routines in LAPACK for this purposes. What you get is 1) A basis for the subspace spanned by the set of input vectors. 2) A basis for the complementary space, which is what you are looking for. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Apr 8 12:16:10 1999 Received: from org.chem.msu.su (org.chem.msu.su [158.250.32.94]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA13758 Thu, 8 Apr 1999 12:16:03 -0400 (EDT) Received: from localhost (serge@localhost) by org.chem.msu.su (8.8.8/8.8.8) with SMTP id UAA09064 for ; Thu, 8 Apr 1999 20:16:01 +0400 (MSD) (envelope-from serge@org.chem.msu.su) Date: Thu, 8 Apr 1999 20:16:01 +0400 (MSD) From: Serge Pissarev Reply-To: Serge Pissarev To: Computational Chemistry List Subject: Molden under Win32 - a summary.. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers! Recently I've posted a question about MOLDEN under NT. I thank all who responded to me: Alexander Likholyot, Artem Masunov, Fabien Borget, Pablo Victoria Garcia and of course the author of MOLDEN Greg Schaftenaar and the developer of MOLDEN for Windows Alexander Klinsky. The home page is They pointed out to me that there are no ports of MOLDEN under Win32 except using the X-server program (MI/X from TNT of another). Well... may be the Win32 port of MOLDEN without X-server to appear soon :) With best regards -- Serge From chemistry-request@www.ccl.net Thu Apr 8 12:45:44 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA13993 Thu, 8 Apr 1999 12:45:43 -0400 (EDT) Received: by bioc1.msi.com (940816.SGI.8.6.9/930416.SGI) id JAA28624; Thu, 8 Apr 1999 09:44:25 -0700 Received: from mica.msi.com(146.202.6.217) by bioc1.msi.com via smap (V2.0) id xma028618; Thu, 8 Apr 99 09:44:22 -0700 Received: from WALDMAN-PC.msi.com by mica.biosym.com.msi.com (4.1/SMI-4.1) id AA01821; Thu, 8 Apr 99 09:50:16 PDT Message-Id: <3.0.32.19990408094108.006d1bd8@146.202.6.217> X-Sender: marvin@146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 08 Apr 1999 09:45:42 -0700 To: chemistry@www.ccl.net From: Marvin Waldman Subject: Re: [Fwd: CCL:Plotting 2D or 3D data and seeing chemical structure] Cc: ericj@msi.com, tvd@msi.com Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" The capabilities requested are available in the C2.QSAR+ product from MSI. By saving the XYZ data in tab delimited format from Excel, they can then be read into the QSAR Study Table along with the structures from the SD file, and then the 2D and 3D plotting capabilities available in the QSAR+ package can be used to perform the desired tasks. On 5-Apr-99, Bruce Wilson wrote: > >From: bewilson@eastman.com ("Wilson, Bruce E") >Subject: CCL:Plotting 2D or 3D data and seeing chemical structure >Date: Mon, 05 Apr 1999 22:22:43 GMT >Approved: CHEMISTRY@ccl.net > >We have a need to be able to display some 2D (and preferably >3D) data in a graph and we need to be able to somehow click >on a point and see the chemical structure associated with >that point. We have a fairly large number of data points, >currently in SD files and some in PDB format, so structure >import is an issue. The XYZ data is currently in Excel. > >A robust, commercial solution is preferred, but I'd >consider freeware/university-ware if it does this one >simple job well. Thanks for any leads and/or information >about products you've tried and liked (or tried and >despised). > > >====================================================== >Bruce E. Wilson (bewilson@eastman.com) >Eastman Chemical Company, Chemicals Research Division >Lincoln St, B-150B, Box 1972 >Kingsport, TN 37662-5150, USA >Office: (423) 229-8886; FAX: (423) 229-4558 Marvin Waldman, Ph.D. Senior Director, Rational and Combinatorial Drug Design Molecular Simulations Inc. e-mail: marvin@msi.com Web: http://www.msi.com Phone: (619) 799-5302 <------------ NOTE NEW PHONE PREFIX FAX: (619) 458-0136 From chemistry-request@www.ccl.net Thu Apr 8 13:14:45 1999 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA14192 Thu, 8 Apr 1999 13:14:44 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id KAA02815 for ; Thu, 8 Apr 1999 10:14:46 -0700 (PDT) Date: Thu, 8 Apr 1999 10:14:45 -0700 (PDT) From: "Dale A. Braden" To: cclpost Subject: orientational averaging Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I want to write a program to calculate neutron scattering intensities from a sample of vibrating molecules. The molecules are randomly oriented, so an orientational average of the molecule with respect to the scattering vector, Q, must be performed. Due to certain experimental details, the direction of Q is actually fixed, and only its magnitude changes. Because the specification of the molecule's orientation and normal mode eigenvectors require many coordinates, it is easier to perform the orientational average by rotating Q with respect to a fixed molecular frame, rather than vice versa. Normally, an orientational average requires the use of 3 Euler angles, but in this case, I think only 2 angles are needed, because Q is a vector and not another 3-dimensional entity. Is this correct? So if my scattering function is S(theta,phi,nu), theta is the angle between Q and the z-axis of my molecular reference frame, phi is the precession angle about z, and nu is the vibrational frequency, then the orientational average should be just Integral[ S(theta,phi,nu) sin(theta) d_theta d_phi ] with theta integrated from 0 to Pi and phi integrated from 0 to 2*Pi. Right? I've looked through many books and articles on this subject, and all agree that the orientational average must be performed, but none give any details. Best wishes, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu