From chpajt@bath.ac.uk Thu Mar 21 05:17:46 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.1/950822.1) id EAA03104; Thu, 21 Mar 1996 04:32:17 -0500 (EST) Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Thu, 21 Mar 1996 09:32:00 +0000 Date: Thu, 21 Mar 1996 09:31:54 +0000 (GMT) From: A J Turner To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net, topper@cooper.edu, freeman@mozart.chm.uri.edu, truhlar@t1.chem.umn.edu Subject: Appology In-Reply-To: <199603202105.AA29564@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am sorry for the incorrect subject line of my previous message. I pressed the wrong button (again!). All the best Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From chpajt@bath.ac.uk Thu Mar 21 05:18:05 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.1/950822.1) id EAA03098; Thu, 21 Mar 1996 04:31:05 -0500 (EST) Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Thu, 21 Mar 1996 09:30:57 +0000 Date: Thu, 21 Mar 1996 09:30:43 +0000 (GMT) From: A J Turner To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net, topper@cooper.edu, freeman@mozart.chm.uri.edu, truhlar@t1.chem.umn.edu Subject: Re: CCL:WWW Molecular Monte Carlo Page In-Reply-To: <199603202105.AA29564@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am interested in the Monticarlo driving routine. IE I give it energy and gradients - and it comes back with a step vector. Does anyone know of a public domane version of such a thing. Also - has anyone done Monticarlo with Charmm? Thanks in advance Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From Jeffrey.Gosper@brunel.ac.uk Thu Mar 21 08:26:36 1996 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.1/950822.1) id HAA04804; Thu, 21 Mar 1996 07:19:08 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Thu, 21 Mar 1996 12:18:16 +0000 Date: Thu, 21 Mar 1996 12:18:14 GMT From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:File format question To: insenk cc: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Fri, 15 Mar 1996 17:59:55 -0500 insenk wrote: > > I am trying to prepare a somewhat special picture with XMol. To do so > I must be able to feed connectivity information into the program. > But the only two file formats understood by XMol for which I have > documentation are PDB and XYZ. XYZ does not allow connectivity > data, and the PDB connectivity records seem to be ignored by XMol. > > Therefore I am looking for a file format that satisfies the following > requirements: > 1) It is understood by XMol, including connectivity information. > 2) Its description is publicly available. > > Any help would be greatly appreciated. Maybe you should try Re_View instead which allows bonding information to be altered by the user. See below for details. If this is not good enough the latest (yet unreleased version) can read in connectivities and bond order information. If your interested in further information please contact me. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From owner-chemistry@ccl.net Thu Mar 21 08:26:42 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id HAA06256; Thu, 21 Mar 1996 07:54:35 -0500 (EST) Received: from focus.ftn.net for amt@ftn.net by bedrock.ccl.net (8.7.1/950822.1) id HAA05841; Thu, 21 Mar 1996 07:54:33 -0500 (EST) Received: from 172.27.99.1 by focus.ftn.net with smtp (Smail3.1.28.1 #7) id m0tzjtY-000NxSC; Thu, 21 Mar 96 07:55 EST Message-Id: Date: Thu, 21 Mar 96 07:55 EST X-Sender: amt@172.27.99.1 (Unverified) X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: amt@ftn.net (Adi Treasurywala) Subject: FINAL call for Validation Symposuim =============================================================== Abstract deadline: April 19 on official ACS abstract form. ACS abstract forms may be requested from (1) http://www.acs.org/memgen/meetings/abrqst.htm (2) Ann Nelson (a_nelson@acs.org) (3) one of the organizers. =============================================================== -- Final call for papers -- VALIDATION METHODS IN COMPUTATIONAL CHEMISTRY American Chemical Society COMP Division 212th National Meeting Orlando, Florida August 25-29, 1996 What we are hoping to highlight through this Symposium is how experts evaluate the relevance and the completeness of a validation experiment in Comp Chem. All aspects of this topic are welcome from software release validation to validation of the results of a particular experiment etc. We hope to have some good examples to offer of the choices of positive and negative controls in such experiments. If you are planning to make a presentation in this symposium please ensure that your abstract reaches one of us on the official abstract form **BEFORE** the deadline. It will be very difficult or impossible to add you in if this is not done. If you are one of those who has already written in earlier asking if you could be a part of this symposium please go ahead and send in an abstract. We will do our best to fit you in. The response to this one has been large-to-overwhelming and we both thank you for that. Dr. A.M.Treasurywala Dr.E.P.Jaeger Allelix Biopharm Inc., 3D Pharm. 6850 Goreway Drive, Eagleview Corporate Center Mississauga Ont 665 Stockton Drive Suite 104 L4V 1V7 CANADA Exton PA 19341 amt@ftn.net jaeger@3dp.com (905)6770831 (610)4586052 FAX (905)6779595 FAX (610)4588249 ******************************** All views expressed here are only my own. Adi M Treasurywala Allelix Biopharma., 6850 Goreway Drive, Mississauga, Ontario. CANADA L4V 1V7. (905)677-0831 FAX (905)677-5344 ******************************** From hinsenk@ERE.UMontreal.CA Thu Mar 21 15:17:53 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id OAA14427; Thu, 21 Mar 1996 14:38:06 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id JAA14767 (8.6.11/IDA-1.6 for ); Thu, 21 Mar 1996 09:28:43 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA11403; Thu, 21 Mar 1996 09:28:06 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id JAA20424; Thu, 21 Mar 1996 09:26:14 -0500 Date: Thu, 21 Mar 1996 09:26:14 -0500 Message-Id: <199603211426.JAA20424@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@www.ccl.net Subject: Connectivity in XMol From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) A few days ago I asked about ways to feed a bond list into XMol for display. Judging from the many responses I received, this seems to be a popular problem. The solution that worked best for me is to load the structure in whatever format into XMol, save in Alchemy format, edit the bond list in the Alchemy file, and load it back into XMol. While no one seems to have a precise description of the Alchemy format, its structure is rather obvious and I had no problems in modifying it. The second most frequently proposed method was to add more atom types and adjust their radii to make the bonds come out correctly. But for my application, and probably for most others, this procedure is a lot more tedious than the previous one. Thanks to everyone who responded to my question. ------------------------------------------------------------------------------- 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) -------------------------------------------------------------------------------