From toukie@zui.unizh.ch Tue Jul 14 08:13:22 1998 Received: from zzmkgtw.zzmk.unizh.ch (zzmkgtw.unizh.ch [130.60.67.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA12497 Tue, 14 Jul 1998 08:13:21 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA20742; Tue, 14 Jul 1998 14:13:20 +0200 Message-Id: <3.0.3.32.19980714141726.0068929c@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Tue, 14 Jul 1998 14:17:26 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: 3D RNA sequence search Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; A co-worker has asked me to post the following message. I hope that some knowledgeable subscriber(s) to this list will see fit to reply. "I have obtained a particular 20-ribonucleotide sequence, and wish to know whether there are any databases containing three-dimensional (crystallographic) 16S bacterial rRNA structures I can search to determine whether a known 16S rRNA structure contains a ribonucleotide sequence identical or similar to my 20-mer." Kindly direct replies to me at toukie@zui.unizh.ch Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From kchana@camsoft.com Tue Jul 14 10:06:46 1998 Received: from nickel.camsoft.com ([198.112.109.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA13368 Tue, 14 Jul 1998 10:06:45 -0400 (EDT) Message-Id: <199807141406.KAA13368@www.ccl.net> Received: from 198.112.109.100 by nickel.camsoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.2); 14 JUL 98 10:02:30 UT Date: 14 Jul 98 10:07:56 -0400 From: Kam Chana Subject: RE:CCL: looking for molecular modeling program on web or free To: CCL X-Mailer: QuickMail Pro 1.5.2 (Mac) X-Priority: 3 MIME-Version: 1.0 Reply-To: Kam Chana Content-Type: text/plain; charset="US-Ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA13368 Barbara Murray wrote: > I am part of a national committee running an undergraduate > pharmaceutical course on-line in the fall. We will be taking the > students through all the steps that are involved in getting a drug to > market. One of the things we want the students to do is to be able to > draw and look at their chosen molecule in some sort of modeling > program. Now, they don't really need to do calculations on this > molecule; just look at it and move it around. Calculations would only > be icing on the cake. Check out Chem3D at our website www.camsoft.com or www.chem3d.com. ChemOffice Net 4.5 will allow you to sketch molecules in 2D using ChemDraw Net and build 3D models (with a six heavy atom) limit using Chem3D Net. Chem3D Net will also allow visualization (including surface visualization) of molecules stored in various formats. Chem3D Std which is available at the student price of $79 allows model building and 2D to 3D conversion and MM2 calculations. For more information checkout our web site or send email to info@camsoft.com Kam Chana CambridgeSoft Corporation From mattacf@mcmail.CIS.McMaster.CA Wed Jul 15 01:04:19 1998 Received: from mcmail.CIS.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.20.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA19417 Wed, 15 Jul 1998 01:04:19 -0400 (EDT) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.8/8.8.8) with SMTP id BAA18407; Wed, 15 Jul 1998 01:04:18 -0400 (EDT) Date: Wed, 15 Jul 1998 01:04:18 -0400 (EDT) From: "C.F. Matta" To: Yongxing Liu cc: chemistry@www.ccl.net Subject: Re: CCL:Experimental solvation free energy results for biomacromolecules In-Reply-To: <199807102105.RAA28990@mail.wesleyan.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Yongxing, Experimental free energies of transfer of the amino acids side-chains from the vapor phase to aqueous phase (pH 7) can be found in: R. Wolfenden, L. Andersson, P. M. Cullis, and C. C. B. Southgate "Affinities of Amino Acid Side Chains for Solvent Water", Biochemistry 20, 1981, pp.849-855. Take care. Cherif Matta Graduate student Chemistry Department McMaster University Hamilton, Ontario Canada L8S 4M1 On Fri, 10 Jul 1998, Yongxing Liu wrote: > > Dear Friends, > > I would like to know if there is some information about experimental > solvation free energy results for biomacromolecules(peptides, proteins, DNAs > and RNAs). Please e-mail any resources from which I can get the related data. > > Thanks a lot in advance > > -------------------------------------------------------------------------- > Yongxing Liu, Graduate Student | E-Mail: yliu@wesleyan.edu > Department of Chemistry | Tel.:860-685-2777 > Wesleyan University | Fax: 860-685-2211 > Middletown CT 06459 | URL: http://ludwig.chem.wesleyan.edu/yliu > > --------------------------------------------------------------------------- > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- > > From segalemb@usp.br Wed Jul 15 06:34:18 1998 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA20317 Wed, 15 Jul 1998 06:34:16 -0400 (EDT) Received: from usp.br by swan2.uspnet.usp.br (SMI-8.6/SMI-SVR4) id HAA29698; Wed, 15 Jul 1998 07:32:28 -0300 Message-ID: <35AC860D.A59B2591@usp.br> Date: Wed, 15 Jul 1998 07:35:57 -0300 From: Sergio Galembek Reply-To: segalemb@usp.br Organization: Universidade de São Paulo X-Mailer: Mozilla 4.03 [pt] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Q: mean plane for a serie of points Content-Type: multipart/mixed; boundary="------------CB0FD536C8295E137886C86B" Esta é uma mensagem de várias partes no formato MIME. --------------CB0FD536C8295E137886C86B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I need to calculate the mean plane for an arbitrary number of points. Does anyone has a program that make this calculation? Thank you, Sergio --------------CB0FD536C8295E137886C86B Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Cartão para Sergio Emanuel Galembeck Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Sergio Emanuel Galembeck n: Galembeck;Sergio Emanuel org: Laboratório de Modelagem Molecular - FFCLRP-USP adr: Laboratorio de Modelagem Molecular;;Departamento de Quimica - FFCLRP - USP;Ribeirao Preto ;Sao Paulo;14040-901;Brazil email;internet: segalemb@usp.br title: Assistant Professor in Physical Chemistry tel;work: (+55)-16-602-37-65 tel;fax: (+55)-16-633-81-51 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------CB0FD536C8295E137886C86B-- From eugene@liposome.genebee.msu.su Wed Jul 15 11:44:30 1998 Received: from liposome.genebee.msu.su (eugene@liposome.genebee.msu.su [158.250.34.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA22681 Wed, 15 Jul 1998 11:43:34 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id TAA28955; Wed, 15 Jul 1998 19:46:40 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Wed, 15 Jul 1998 19:46:38 +0400 (MSD) To: chemistry@www.ccl.net Subject: BEO:FYI - a panel about Linux, 3-D and OpenGL/Mesa issues at SIGGRAPH In-Reply-To: <9807151440.AA03917@shaman.zk3.dec.com> References: <9807151440.AA03917@shaman.zk3.dec.com> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13740.52669.772228.403471@liposome.genebee.msu.su> Offtopic? I hope not _very_. I'm still looking forward to try out VMD (or gOpenMol) under 3dfx-savvy Mesa. Regards, Eugene Jon 'maddog' Hall, USG Senior Leader writes: > Knowing that some people on these lists are interested in high-performance > 3-D graphics, I am passing on this note to you. > > Daryll Strauss, for those of you who are not familiar with his name, is > one of the brains behind using Linux on the movie "Titanic". He works > for Digital Domain. > > md > ------- Forwarded Message [ header tedium snipped ] > From: Daryll Strauss > To: maddog@li.org > Subject: Linux 3-D SIG at SIGGRAPH > Mime-Version: 1.0 > Content-Type: text/plain; charset=us-ascii > X-Mailer: Mutt 0.91.1 > > Jon, I thought you might find this interesting. We're putting together a > SIG to discuss 3-D under Linux. Here's the announcement. > > Brian Paul and I are hosting a SIG session at SIGGRAPH '98 to > discuss Linux, 3-D, and OpenGL/Mesa issues. The goals of the session are > to present the current state of 3-D under Linux, to attract new > developers, to get feedback from the user community, and to allow > vendors to gauge the interest. So, if you're interested in freely > available 3-D please join us: > > Wednesday July 22nd > 6-8 PM > The Peabody Hotel > Plaza Ballroom B > > For more information on the event please see our webpage at: > http://glide.xxedgexx.com/SIGGRAPH.html > > If you are interested in presenting at our session please email to > daryll@harlot.rb.ca.us. > > If you are going to attend, an RSVP is appreciated but not > required. Just drop us a note at linux3d@harlot.rb.ca.us > > We look forward to seeing all of you. > > - |Daryll > > > > > > > ------- End of Forwarded Message > > > -- > ============================================================================= > Jon "maddog" Hall Internet: maddog@zk3.dec.com > Senior Leader, UNIX Software Group Executive Director, Linux International > > Compaq Computer Corporation Linux International > Mailstop ZK03-2/U15 80 Amherst St. > 110 Spit Brook Rd. Amherst, N.H. 03031-3032 U.S.A. > Nashua, N.H. 03062-2698 U.S.A. > > WWW: http://www.compaq.com WWW: http://www.li.org > Voice: +1.603.884.1341 Voice: +1.603.672.4557 > FAX: +1.603.884.6424 Board Member: Uniforum Association > Office: ZK03-2/V15 Board Member: USENIX Association > From noertema@theochem.tu-muenchen.de Wed Jul 15 11:56:51 1998 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA22747 Wed, 15 Jul 1998 11:56:48 -0400 (EDT) Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id RAA13602 for ; Wed, 15 Jul 1998 17:56:29 +0200 Received: by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id RAA00050; Wed, 15 Jul 1998 17:56:36 +0200 Date: Wed, 15 Jul 1998 17:56:36 +0200 From: noertema@theochem.tu-muenchen.de (Folke Noertemann) Message-Id: <199807151556.RAA00050@theo3.theochem.tu-muenchen.de> To: chemistry@www.ccl.net Subject: BFGS vs. DFP X-Sun-Charset: US-ASCII Dear CCL'ers, I have a question concerning the update algorithms used for the Hessian during optimizations and transition state searches. In a paper by J.Baker (J.Comp.Chem 7, 385-395 (1986)) and some manuals (Gamess, Gaussian) the statement is made that while the BFGS update is *better* for an optimization, for a transition state search the DFP update is to be preferred. Of course, no reason is provided to support this statement. One of the books frequently referred to (Fletcher: Practical Methods of Optimization) makes the following statements: - Provided that the function being optimized is quadratic AND the line-search is exact, positive definiteness of the Hessian is preserved (for both DFP and BFGS formulas) - For inexact line searches, global convergence of the BFGS method has been proved. However, for the DFP this could not be shown. Is this somehow related to the fact that for TS searches, the DFP-method is recommended? Why is this so? Does this mean that the BFGS method will lead to a positive-definite Hessian, even if the the initial Hessian has the required negative eigenvalue ? Any hint is appreciated! Thanks, F. Noertemann Folke Noerteman Lehrstuhl f. Theoret. Chemie TU Muenchen noertema@theochem.tu-muenchen.de