From chemistry-request@server.ccl.net Tue Feb 18 04:30:28 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1I9URI31663 for ; Tue, 18 Feb 2003 04:30:27 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id JAA79841; Tue, 18 Feb 2003 09:41:27 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18l40N-0002Ds-00; Tue, 18 Feb 2003 09:25:35 +0000 Date: Tue, 18 Feb 2003 09:25:35 +0000 (GMT) From: Szilveszter Juhos To: "Dr. N. V. Sastry" cc: chemistry@ccl.net Subject: Re: CCL:Request for the values of Free Energy of Hydration for alkane diols In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 17 Feb 2003, Dr. N. V. Sastry wrote: > hydration for various salkane diols such as 1,2-ethane diol (ethylene glycol) -9.3 kcal/mol Chambers et al J Phys Chem 1996 100:16385-16389 They are referring to quite a few experimental sources. Hope it helps: Szilva From chemistry-request@server.ccl.net Tue Feb 18 03:23:35 2003 Received: from vspnt017.isiconsulting.it ([213.140.25.217]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1I8NZI18176 for ; Tue, 18 Feb 2003 03:23:35 -0500 Received: by smtp.xelionfinancialstudio.it with Internet Mail Service (5.5.2650.21) id ; Tue, 18 Feb 2003 09:23:34 +0100 Message-ID: <5C1E071BB0B1E4449C53F68EEF7DF47F0D5BB5@vspw2217.getracenter.it> From: Forlani Roberto To: "'chemistry@ccl.net'" Subject: 2D beautify # Summary Date: Tue, 18 Feb 2003 09:23:34 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear all, yesterday I've send the following question to this mailing list: >-----Original Message----- >From: Forlani Roberto >Sent: Monday, February 17, 2003 2:41 PM >To: chemistry@ccl.net >Subject: 2D beautify > > >Dear CCLers, > > I wonder if anyone could tell me of any method to "beautify" a 3D multi sdf file >into a 2D multi sdf file. >I'll summarize. > >Very best, > >Roberto I would like to thank all the following people for their kind answers and Dimitris Agrafiotis for his courtesy. I've really appreciated. Best regards, Roberto Forlani - Didier Rognan CLIFF, which is distributed by Molecular Networks (http://www.mol-net.de/) does that job. - Mireille Krier I recently came around CLIFF , a program for interconversion of chemical structure exchange file formats for compounds and reactions. You can get a trial version from Molecular Network http://www.mol-net.de The command-line will be: cliff -outfile nice.sdf -recalc 1 ugly.mol - Egon Willighagen CDK can do this. (http://cdk.sf.net/). It has a opensource layout engine that generates 2D coordinates. - Leif Norskov Within the Unity suite of programs from Tripos there are tools (e.g. dbtranslate) that will do what you ask for. Quite well, and quickly too. - Ajit Jadhav Several tools such as cactvs will do 2d beautification (regardless of providing 3d coordinates or just SLNs). For a recent review on methods, see: Rev in Comp Chem v13 - Harold E. Helson, Structure Diagram Generation, pp. 313-398 http://chem.iupui.edu/~boyd/rccontents.html - Marc Nicklaus You should be able to do this with our web service at http://cactus.nci.nih.gov/services/translate/. I don't remember if we recalculate (beautified) 2D coordinates when you read in a multi-structure 3D SD file and request 2D SDF as the output, or if we simply zero out the z coordinates. Should the latter be the case, you should be able to achieve your goal in a two-step process: First export your structures as a (multi-structure) SMILES file; then re-import *that*, and choose 2D SDF as the output format. This will guarantee that 2D coordinates are recomputed. Let me know if you experience problems with this. These are CACTVS-calculated coordinates. You could of course use the CACTVS toolkit itself (in various ways) to do the beautification. - Doug Henry I think that MDL (Business Rules Interface), Daylight (DEPICT), and Marvin Applets all provide this functionality. The Exographics Chemeleon program can convert from various file formats - one could for instance, convert to multi-SMILES file, then convert back to sdf and the program will assign 2D coords. - L. Shyamal One way to force the molecules into neat 2D structures, would be to convert all the molecules in the the SDF to SMILES and then use a SMILES to MOL converter, most of them have a de-novo 2D diagram layout algorithm built into them From chemistry-request@server.ccl.net Tue Feb 18 06:37:29 2003 Received: from typhoeus.chem.york.ac.uk ([144.32.72.225]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1IBbTI01250 for ; Tue, 18 Feb 2003 06:37:29 -0500 Received: from ysbl.york.ac.uk (rasher [144.32.20.17]) by typhoeus.chem.york.ac.uk (8.11.6+Sun/8.11.6) with ESMTP id h1IBbUQ23148 for ; Tue, 18 Feb 2003 11:37:30 GMT Sender: greaves@ysbl.york.ac.uk Message-ID: <3E521AFA.E31D0D0@ysbl.york.ac.uk> Date: Tue, 18 Feb 2003 11:37:30 +0000 From: Richard Greaves Reply-To: greaves@ysbl.york.ac.uk Organization: York Structural Biology Laboratory X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: DOZRF in pKa calculations using UHBD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I am trying to run pKa calculations on several insulin hexamer models to investigate the effect of mutations on the ionization behaviour of a key acidic residue. Each model is essentially the same as the others except at the single residue where the mutation has been made. I am using exactly the same set up for each model and all but one of my calculations have run to successful completion. However, one calculation fails. I can run the dosbsvscal script on the model at the required dielectric settings ( I chose 78.0 for solvent and 8.5 for the protein ) but for just this one model the 'potentials' file generated for the low dielectric/zero ionic strength run causes hybrid_jan2new2 to stall. However, if I use a value of 8.0 for this dielectric then the calculation runs OK. Why can't I use 8.5 as my dielectric value for this system? Richard Greaves. From chemistry-request@server.ccl.net Tue Feb 18 10:21:30 2003 Received: from facepe.dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1IFLTI05214 for ; Tue, 18 Feb 2003 10:21:30 -0500 Received: from dqf.ufpe.br ([150.161.5.23]) by facepe.dqf.ufpe.br (8.12.6/8.12.6) with ESMTP id h1ICwaWT012282 for ; Tue, 18 Feb 2003 09:58:36 -0300 (BRT) (envelope-from mozart.pimentel@dqf.ufpe.br) Message-ID: <3E52445F.5030707@dqf.ufpe.br> Date: Tue, 18 Feb 2003 11:34:07 -0300 From: Mozart Pimentel User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021130 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ZINDO/S and Sr. Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dears CCL'ers, Does anyone know if there are parameters for Sr implemented in ZINDO/S? ECP's are welcome too. Thanks. From chemistry-request@server.ccl.net Tue Feb 18 11:39:05 2003 Received: from vmail.mclink.it ([195.110.128.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1IGd4I06567 for ; Tue, 18 Feb 2003 11:39:04 -0500 Received: from Mitac (net203-175-121.mclink.it [213.203.175.121]) by vmail.mclink.it (8.11.3/8.11.3) with SMTP id h1IGd1g06301 for ; Tue, 18 Feb 2003 17:39:02 +0100 (CET) (envelope-from elena.fioravanzo@chimici.it) From: "Elena Fioravanzo" To: "CCL" Subject: conformational analysis Date: Tue, 18 Feb 2003 17:42:56 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear all, I would like to compare different conformational analysis methods. Is there a standard structures set I may use? May I find somewhere in the web the experimental 3D structures to use as reference? I thank you in advance for your answer, best regards Elena ------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 347 4054991 Fax ++39 0444 533954 E-mail support@s-in.it Web http://www.s-in.it/ From chemistry-request@server.ccl.net Tue Feb 18 19:28:08 2003 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1J0S7I14991 for ; Tue, 18 Feb 2003 19:28:07 -0500 Received: from mserv.itpa.lt (localhost [127.0.0.1]) by mserv.itpa.lt (8.12.6/8.12.6) with ESMTP id h1J0S6Tl088367 for ; Wed, 19 Feb 2003 02:28:06 +0200 (EET) (envelope-from tamulis@mserv.itpa.lt) Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.12.6/8.12.6/Submit) with ESMTP id h1J0S67i088364 for ; Wed, 19 Feb 2003 02:28:06 +0200 (EET) Date: Wed, 19 Feb 2003 02:28:06 +0200 (EET) From: Arvydas Tamulis To: chemistry@ccl.net Subject: Rasmol Message-ID: <20030219022546.W88322-100000@mserv.itpa.lt> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Would you please to inform me where are located Rasmol programs (say few ftp servers). Best regards, Arvydas Tamulis ******************************************************************* Temporal address until 30 April 2004: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: 1 505 667-7278 Fax: 1 505 665-2659 e-mail: tamulis@cnls.lanl.gov ******************************************************************* From chemistry-request@server.ccl.net Tue Feb 18 20:07:57 2003 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1J17vI15334 for ; Tue, 18 Feb 2003 20:07:57 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Tue, 18 Feb 2003 20:07:53 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Tue, 18 Feb 2003 20:07:36 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:Rasmol Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h1J17vI15335 Arvydas: You can get Rasmol, and more, at: http://www.umass.edu/microbio/rasmol/ Pete Gannett >>> Arvydas Tamulis 02/18/03 07:28PM >>> Dear Netters, Would you please to inform me where are located Rasmol programs (say few ftp servers). Best regards, Arvydas Tamulis ******************************************************************* Temporal address until 30 April 2004: Los Alamos National Laboratory Center for Nonlinear Studies P.O. Box 1663, Mail Stop B258 Los Alamos, New Mexico 87545 Work Phone: 1 505 667-7278 Fax: 1 505 665-2659 e-mail: tamulis@cnls.lanl.gov ******************************************************************* -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net