From chemistry-request@ccl.net Wed Dec 1 10:42:09 2004 Received: from prg.traveller.cz (prg.traveller.cz [193.85.2.77]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1Fg8Eo016267 for ; Wed, 1 Dec 2004 10:42:09 -0500 Received: from ntt ([193.85.250.178]) by prg.traveller.cz (8.13.1/8.13.1/prg) with SMTP id iB1Fuq04006912 for ; Wed, 1 Dec 2004 16:56:57 +0100 (CET) Message-ID: <005401c4d7be$69a38a20$c964a8c0$at$spechem.cz> From: "Jiri Krechl" To: Subject: CCL: smiles to sdf converter Date: Wed, 1 Dec 2004 16:57:00 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1250" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 I am looking for a smiles to sdf converter able to run on PC/Win. Apparently Babel might be the solution but the last version I could found for DOS environment (babel16) does not seem to support smiles among otherwise wide variety of input/output formats. Thanks for a hint. Jiri e: jiri.krechl$at$spechem.cz --- Outgoing mail is certified Virus Free. Zkontrolovano antivirov}m systimem AVG (http://www.grisoft.cz). Verze: 6.0.802 / Virova baze: 545 - datum vydanm: 26.11.2004 From chemistry-request@ccl.net Wed Dec 1 05:27:43 2004 Received: from web14426.mail.yahoo.com (web14426.mail.yahoo.com [216.136.175.187]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iB1ARgYh031701 for ; Wed, 1 Dec 2004 05:27:42 -0500 Received: (qmail 85556 invoked by uid 60001); 1 Dec 2004 10:42:30 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=FVaUgQQL9KGVo3Rw3R7vKqyb4x8YBNGvfKYw/slumn08TeyeY88eNwJfVyi7cylL5NHZRq6kEZPQLm//yHFzOa7DmLCmISutQsZVglLJe1WBRwm1td7hrdtAkLCVMfQ0L2gnSBlX9HKRt7/dooRaJUgWMZ05CXGDm6tlFJZ/x0Q= ; Message-ID: <20041201104230.85554.qmail(at)web14426.mail.yahoo.com> Received: from [84.66.141.119] by web14426.mail.yahoo.com via HTTP; Wed, 01 Dec 2004 02:42:30 PST Date: Wed, 1 Dec 2004 02:42:30 -0800 (PST) From: Ricardo Oliveira Subject: CCL: question on TDDFT using Gaussian 03 To: chemistry(at)ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=3.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR, NORMAL_HTTP_TO_IP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello everyone, I am having a problem with identifying those numbers on the right hand side of the transitions. Below there is an extract from an output file from a TDDFT (LSDA) calculation on pyridine.*************************** Excited State 3: ?Spin -A' 4.5362 eV 273.32 nm f=0.0016 22A -> 26A 0.79830 20B -> 22B 0.60419 21B -> 23B -0.25908 *********************** The number of the excited state (3) along with its energy (4.5362 eV) and corresponding wavelength are given above. The letter f represents the oscillator strenght. The question is: what are those other 3 numbers : 0.79830 0.60419 -0.25908 ?? Regards and thanks _________________________ Ricardo Oliveira University of Sussex School of Life Sciences Chichester 3R 504 phone: (44) 1273678419 email: kau43(at)sussex.ac.uk web: http://84.66.141.119/sitePhD/indexl.htm Falmer - Brighton UK __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com From chemistry-request@ccl.net Wed Dec 1 03:20:21 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB18KJE0025214 for ; Wed, 1 Dec 2004 03:20:20 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/4.23) with ESMTP id iB18Z2rb001547; Wed, 1 Dec 2004 09:35:02 +0100 (MET) From: "E.L. Willighagen" Reply-To: e.willighagen*at*science.ru.nl To: "Renxiao Wang" Subject: Re: CCL:Software for pattern recognition in QSAR studies? Date: Wed, 1 Dec 2004 09:34:59 +0100 User-Agent: KMail/1.6.2 Cc: References: In-Reply-To: MIME-Version: 1.0 Content-Disposition: inline Content-Type: Text/Plain; charset="iso-8859-1" Message-Id: <200412010935.01453.e.willighagen*at*science.ru.nl> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB18KLE0025215 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Monday 29 November 2004 20:58, Renxiao Wang wrote: > I am looking for a program that can apply standard pattern recognition > techniques. Basically, I want to study a number of samples, each of > which can be characterized by some properties. I would like to classify > these samples into several groups based on these properties, and then > derive a QSAR model for each group. > > So, I would like to try some popular software in this area for the > clustering purpose. If you have any clue, please kindly let me know, and > I will put back the summary shortly. Use R: http://www.r-project.org/ Egon - -- e.willighagen*at*science.ru.nl PhD-student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBrYI0d9R8I9Yza6YRAligAJ9v5ro5o3Dyk9BqIcj/LtEWuY6zeQCdHhah b09HXYQlq2+gROso1jn/2r0= =N2K3 -----END PGP SIGNATURE----- From chemistry-request@ccl.net Wed Dec 1 11:23:23 2004 Received: from ballard.acpub.duke.edu (ballard.acpub.duke.edu [152.3.233.84]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1GN2f6018400 for ; Wed, 1 Dec 2004 11:23:07 -0500 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by ballard.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id iB1GbdSW003777 for ; Wed, 1 Dec 2004 11:37:40 -0500 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id iB1GbfO1027014; Wed, 1 Dec 2004 11:37:41 -0500 (EST) Date: Wed, 1 Dec 2004 11:37:41 -0500 (EST) From: jz7-.at.-duke.edu Sender: jz7-.at.-duke.edu To: CHEMISTRY-.at.-ccl.net Subject: how to print Fock matrix in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.6.1.107272, Antispam-Core: 4.6.1.106808, Antispam-Data: 2004.11.30.24 X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, How should I write the command line to print the Fock matrix using INDO method in Gaussian (just a single point calculation)? Thanks a lot! From chemistry-request@ccl.net Wed Dec 1 10:33:07 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1FX6Eo015781; Wed, 1 Dec 2004 10:33:07 -0500 To: "Renxiao Wang" Cc: chemistry{at}ccl.net, "Computational Chemistry List" Subject: Re: CCL:Software for pattern recognition in QSAR studies? MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy{at}givaudan.com Date: Wed, 1 Dec 2004 16:47:52 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 01/12/2004 16:47:55, Serialize complete at 01/12/2004 16:47:55 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iB1FX7Eo015782 Dear Dr. Wang, For unsupervised pattern recognition, please try: 1. DISTILL in Sybyl, 2. MOLOC 3 ClassPharmer 4. Jchem from Chemaxon. For supervised pattern recognition, please try: 1. SIMCA in Sybyl 2. Recursive Partitioning (RP) in Cerius2 3. RP in ClassPharmer 4. LDA in TSAR 5. Binary QSAR in MOE. Best regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy{at}givaudan.com "Renxiao Wang" Sent by: "Computational Chemistry List" 29.11.2004 20:58 To: cc: Subject: CCL:Software for pattern recognition in QSAR studies? Dear all, I am looking for a program that can apply standard pattern recognition techniques. Basically, I want to study a number of samples, each of which can be characterized by some properties. I would like to classify these samples into several groups based on these properties, and then derive a QSAR model for each group. So, I would like to try some popular software in this area for the clustering purpose. If you have any clue, please kindly let me know, and I will put back the summary shortly. Best regards, Renxiao -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao{at}med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow{at}nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Dec 1 13:37:30 2004 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1IbSH9028495 for ; Wed, 1 Dec 2004 13:37:28 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id iB1HYge07210; Wed, 1 Dec 2004 10:34:42 -0700 Message-ID: <41AE12D1.6080807!at!eyesopen.com> Date: Wed, 01 Dec 2004 11:52:01 -0700 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jiri Krechl , CHEMISTRY!at!ccl.net Subject: Re: CCL:smiles to sdf converter References: <005401c4d7be$69a38a20$c964a8c0!at!spechem.cz> Content-Type: text/plain; charset=windows-1250; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.9 required=7.5 tests=MY_DSL,NO_COST autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > I am looking for a smiles to sdf converter able to run on PC/Win. What do you mean by SMI to SDF conversion? For what purpose? You can use the babel2 script that is shipped with the OEChem Toolkit to make the direct conversion. The information will be put into the right format, but the coordinates will be 0.00 because SMI actually doesn't have any coordinate information. [Matt Stahl, who wrote Babel with Pat Walters, is one of the authors of OEChem]. You can use OGHAM to convert SMI into 2D coordinates suitable for depiction (and also do the depictions). If you want to generate 3D coordinates check out OMEGA, which will generate full conformational ensembles. All of our software runs on a multitude of platforms, including Windows. More information on all three is at http://www.eyesopen.com/products/ It's not clear from your signature where you are working, but for non-commercial use, all OpenEye software is available at no charge. Regards, George Vacek VP, Business Development OpenEye Scientific Software vacek!at!eyesopen.com 505.473.7385 ********************************************************************* OpenEye recently announced the following software releases: EON 1.0, WABE 1.3, QUAC PAC 1.1, OMEGA 1.8, FRED 2.0 http://www.eyesopen.com/about/news/press_releases/ ********************************************************************* From chemistry-request@ccl.net Wed Dec 1 13:53:56 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1IriH9029034 for >ccl.net>; Wed, 1 Dec 2004 13:53:55 -0500 Received: from solo.sci.kun.nl [131.174.16.134] (helo=sci.kun.nl) by wn1.sci.kun.nl (8.12.10/4.23) with ESMTP id iB1J8Urg011082; Wed, 1 Dec 2004 20:08:30 +0100 (MET) From: Egon Willighagen >science.ru.nl> Reply-To: e.willighagen<>science.ru.nl To: "Jiri Krechl" >spechem.cz> Subject: Re: CCL:smiles to sdf converter Date: Wed, 1 Dec 2004 20:08:29 +0100 User-Agent: KMail/1.7.1 Cc: CHEMISTRY<>ccl.net References: <005401c4d7be$69a38a20$c964a8c0<>spechem.cz> In-Reply-To: <005401c4d7be$69a38a20$c964a8c0<>spechem.cz> MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1250" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200412012008.29984.e.willighagen<>science.ru.nl> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wednesday 01 December 2004 16:57, Jiri Krechl wrote: > I am looking for a smiles to sdf converter able to run on PC/Win. > Apparently Babel might be the solution but the last version I could found > for DOS environment (babel16) does not seem to support smiles among > otherwise wide variety of input/output formats. A few opensource options: OpenBabel: http://openbabel.sf.net/ JOELib: http://joelib.sf.net/ Chemistry Development Kit: http://cdk.sf.net/ kind regards, Egon -- e.willighagen<>science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From chemistry-request@ccl.net Wed Dec 1 15:13:49 2004 Received: from web53910.mail.yahoo.com (web53910.mail.yahoo.com [206.190.36.220]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iB1KDmH9032382 for >ccl.net>; Wed, 1 Dec 2004 15:13:48 -0500 Received: (qmail 20696 invoked by uid 60001); 1 Dec 2004 20:28:34 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=Q9WE/SBmjHOH/rx75ey8KMPfxMDYf5JEE+mIc2i+vCvEpOmggyo3lFd8zvGs/ppKejZB47BL1mIJTomd7AvNJExv9KCZMYushnj3UJUdbCKKyA0BDSoPUFZNCKbpy7zjGf+SeX6Ovu9vjDw2W5nztyV3iv8o4RM2gN/ZNtDRllo= ; Message-ID: <20041201202834.20694.qmail=at=web53910.mail.yahoo.com> Received: from [129.109.59.107] by web53910.mail.yahoo.com via HTTP; Wed, 01 Dec 2004 12:28:34 PST Date: Wed, 1 Dec 2004 12:28:34 -0800 (PST) From: IEJMD Subject: IECMD 2004 - November 29 - December 12 To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Internet Electronic Conference of Molecular Design 2004 IECMD 2004, November 29 - December 12 http://www.biochempress.com http://groups.yahoo.com/group/iecmd2004 Hi, The Internet Electronic Conference of Molecular Design 2004, IECMD 2004, consists of ten sessions, i.e. November 29 - December 3 and December 6 - December 10. The Conference program and accepted papers are posted on the Web at http://www.biochempress.com Four to five papers are scheduled for discussion and questions in each session. The discussions of the IECMD 2004 papers will take place on the Web, using the Yahoo! group IECMD 2004, http://groups.yahoo.com/group/iecmd2004 Everyone is encouraged to submit comments and questions to iecmd2004=at=yahoogroups.com Confidential comments can be submitted to iejmd=at=yahoo.com Conference participants can choose to read the comments at the Conference site (http://groups.yahoo.com/group/iecmd2004), to receive them by E-mail, or both. Please note that you can control whether or not you receive posts by E-mail; just log-in to your account from the Yahoo! group IECMD 2004 (http://groups.yahoo.com/group/iecmd2004) and make the appropriate changes. I am looking forward to your participation in IECMD 2004 and the Conference proceedings. Best regards, John Paul Smith __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Wed Dec 1 13:50:42 2004 Received: from mtaout-m.tc.umn.edu (mtaout-m.tc.umn.edu [160.94.23.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1IofH9028943 for ; Wed, 1 Dec 2004 13:50:41 -0500 Received: from pobox.com (abacavir.pharmacy.umn.edu [160.94.172.208] (may be forged)) by mtaout-m.tc.umn.edu with ESMTP; Wed, 1 Dec 2004 13:05:19 -0600 (CST) X-Umn-Remote-Mta: [N] abacavir.pharmacy.umn.edu [160.94.172.208] #+HF+LO+TS+AU Message-ID: <41AE16C4.4030004*at*pobox.com> Date: Wed, 01 Dec 2004 13:08:52 -0600 From: Eric Bennett User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4.1) Gecko/20040326 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY*at*ccl.net CC: Jiri Krechl Subject: Re: CCL:smiles to sdf converter References: <005401c4d7be$69a38a20$c964a8c0*at*spechem.cz> In-Reply-To: <005401c4d7be$69a38a20$c964a8c0*at*spechem.cz> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jiri Krechl wrote: >I am looking for a smiles to sdf converter able to run on PC/Win. Apparently >Babel might be the solution but the last version I could found for DOS >environment (babel16) does not seem to support smiles among otherwise wide >variety of input/output formats. > > > There is a more recent precompiled Windows version of Open Babel (successor to Babel) here: http://cml.sourceforge.net/new/ OpenBabel sort of supports SMILES but according to the docs it sets all the atom coordinates to zero instead of trying to build a reasonable 3D geometry, so it may or may not fit your needs. -- Eric Bennett, Center for Drug Design, U of Minnesota From chemistry-request@ccl.net Wed Dec 1 13:42:24 2004 Received: from ucrwcu.rwc.uc.edu (ucrwcu.rwc.uc.edu [129.137.3.94]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1IgNH9028684 for ; Wed, 1 Dec 2004 13:42:23 -0500 Received: from GREERMD.ucrwcu.rwc.uc.edu (dhcp754.rwc.uc.edu [10.228.83.247]) by ucrwcu.rwc.uc.edu (Postfix) with ESMTP id 6B13018129 for ; Wed, 1 Dec 2004 13:56:35 -0500 (EST) Message-Id: <6.1.2.0.2.20041201135325.01bdb940.-at-.ucrwcu.rwc.uc.edu> X-Sender: greermd.-at-.ucrwcu.rwc.uc.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Wed, 01 Dec 2004 13:57:34 -0500 To: chemistry.-at-.ccl.net From: Melinda Greer Subject: posting - Patterson-Crane Award call for nominations Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_20646906==.ALT" X-Spam-Status: No, hits=0.0 required=7.5 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_20646906==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Can the announcement below be posted on the listserv? Thanks. Melinda Greer, Ph.D. ACS, Dayton Section Chair, Patterson-Crane Award Committee Call for Nominations: The Patterson-Crane Award The Dayton and Columbus Sections of the American Chemical Society sponsor=20 the Patterson-Crane Award for contributions to chemical information. It is= =20 international in scope and given in honor of two outstanding members of the= =20 Sections: Austin M. Patterson (1876=961956) and E.J. Crane (1889=961966). = The=20 biennial award consists of a $2,000 honorarium and a personalized=20 commendation. The award is funded by a bequest of the Patterson family to= =20 the Dayton Section, by the Helen G. Crane Fund of the Columbus Foundation,= =20 and by the Patterson-Crane Award Fund of the Columbus Section. The Austin M. Patterson Award was established in 1949 by the Dayton Section= =20 to acknowledge meritorious contributions in the field of chemical=20 literature and especially documentation of chemistry. Dr. Patterson, the=20 first recipient of the biennial award, was recognized for his leadership in= =20 organic chemical nomenclature and his work as editor of Chemical=20 Abstracts. There were 13 additional recipients of this award, including=20 E.J. Crane, who was editor of Chemical Abstracts from=20 1915=961958. Subsequently, there was a desire to honor and establish an=20 award in his memory. In February 1975 the ACS Board of Directors accepted a= =20 proposal by the Dayton and Columbus Sections for a jointly sponsored=20 Patterson-Crane Award. Award Criteria Nominees, who need not hold ACS membership, should demonstrate outstanding= =20 achievement in the field of chemical information science. Contributions of= =20 international significance may relate to: =B7 Design, development, production, or management of chemical=20 information systems or services. =B7 Electronic access to and retrieval of chemical information;=20 critically evaluated data compilations. =B7 Information technology applications in chemistry or other=20 significant chemical documentation, including production of original works,= =20 editorial work, or chemical library work. Nominations for the award must be in writing and should discuss the=20 nominee's contributions to the field as well as an evaluation of=20 accomplishments. Materials supporting the nomination should include a=20 biography and bibliography of publications and presentations. Seconding=20 letters are required. Send one copy of the nomination materials to Dr. Melinda Greer, Chair of=20 the Patterson-Crane Award Committee, (Raymond Walters College, 9555=20 Plainfield Road, Cincinnati, OH 45236) for receipt by 31 January 2005. To= =20 receive an informative brochure about the award, contact Dr. Greer=20 (513-936-7165 or melinda.greer.-at-.uc.edu). Nominations will be judged by a seven-member selection committee consisting= =20 of Dayton and Columbus Section members as well as the Chair of the American= =20 Chemical Society's Division of Chemical Information. The 2005 Patterson-Crane Award will be presented in the Spring of 2005 at=20 an awards dinner to be held in Dayton, Ohio. --=====================_20646906==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Can the announcement below be posted on the listserv?

Thanks.

Melinda Greer, Ph.D.
ACS, Dayton Section
Chair, Patterson-Crane Award Committee


Call for Nominations: The Patterson-Crane Award
The Dayton and Columbus Sections of the American Chemical Society sponsor the Patterson-Crane Award for contributions to chemical information. It is international in scope and given in honor of two outstanding members of the Sections: Austin M. Patterson (1876=961956) and E.J. Crane (1889=961966).  The biennial award consists of a $2,000 honorarium and a personalized commendation.  The award is funded by a bequest of the Patterson family to the Dayton Section, by the Helen G. Crane Fund of the Columbus Foundation, and by the Patterson-Crane Award Fund of the Columbus Section.
 
The Austin M. Patterson Award was established in 1949 by the Dayton Section to acknowledge meritorious contributions in the field of chemical literature and especially documentation of chemistry.  Dr. Patterson, the first recipient of the biennial award, was recognized for his leadership in organic chemical nomenclature and his work as editor of Chemical Abstracts.  There were 13 additional recipients of this award, including E.J. Crane, who was editor of Chemical Abstracts from 1915=961958.  Subsequently, there was a desire to honor and establish an award in his memory. In February 1975 the ACS Board of Directors accepted a proposal by the Dayton and Columbus Sections for a jointly sponsored Patterson-Crane Award. 
 
Award Criteria
Nominees, who need not hold ACS membership, should demonstrate outstanding achievement in the field of chemical information science.  Contributions of international significance may relate to:
=B7        Design, development, production, or management of chemical information systems or services.
=B7        Electronic access to and retrieval of chemical information; critically evaluated data compilations.
=B7        Information technology applications in chemistry or other significant chemical documentation, including production of original works, editorial work, or chemical library work.
 
Nominations for the award must be in writing and should discuss the nominee's contributions to the field as well as an evaluation of accomplishments.  Materials supporting the nomination should include a biography and bibliography of publications and presentations.  Seconding letters are required.
 
Send one copy of the nomination materials to Dr. Melinda Greer, Chair of the Patterson-Crane Award Committee, (Raymond Walters College, 9555 Plainfield Road, Cincinnati, OH 45236) for receipt by 31 January 2005.  To receive an informative brochure about the award, contact Dr. Greer (513-936-7165 or melinda.greer.-at-.uc.edu).
 
Nominations will be judged by a seven-member selection committee consisting of Dayton and Columbus Section members as well as the Chair of the American Chemical Society's Division of Chemical Information.
 
The 2005 Patterson-Crane Award will be presented in the Spring of 2005 at an awards dinner to be held in Dayton, Ohio.
--=====================_20646906==.ALT-- From chemistry-request@ccl.net Wed Dec 1 16:24:23 2004 Received: from warhawk.mpi.com (gate-us-2.mpi.com [63.244.250.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1LOLH9003744 for ; Wed, 1 Dec 2004 16:24:21 -0500 Received: from lightning.mpi.com (lightning [63.244.252.11]) by warhawk.mpi.com (Switch-3.1.6/Switch-3.1.6) with ESMTP id iB1LdB1m002201 for ; Wed, 1 Dec 2004 16:39:11 -0500 (EST) Received: from US-VS1.corp.mpi.com (us-be1.corp.mpi.com [63.244.252.30]) by lightning.mpi.com (Switch-3.1.6/Switch-3.1.6) with ESMTP id iB1LcZTc005595 for ; Wed, 1 Dec 2004 16:39:07 -0500 (EST) X-MIMEOLE: Produced By Microsoft Exchange V6.0.6603.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4D7EE.121A1C5A" Subject: RE: smiles to sdf converter Date: Wed, 1 Dec 2004 16:38:17 -0500 Message-ID: <9C5166762F311146951505C6790A9CF802EF135A)at(US-VS1.corp.mpi.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: smiles to sdf converter Thread-Index: AcTX7N4wf+30vXYYT/uhsz0r4y0CiAAAF7VA From: "Stradella, Omar" To: X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_60_70,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C4D7EE.121A1C5A Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable C= ORINA will generat= e a 3D SD file from SMILES directly. There's a service, available on the= web, that allow you to use CORINA in that way: http://cactus.nci.nih.gov/services/translate Omar _______________________ Omar Stradella Computational Chemistry Millennium Pharmaceuticals 40 Landsdowne St Cambridge, MA 02139 stradella)at(mpi.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net] = On Behalf Of Eric Bennett Sent: Wednesday, December 01, 2004 2:09 PM To: CHEMISTRY)at(ccl.net Cc: Jiri Krechl Subject: CCL:smiles to sdf converter Jiri Krechl wrote: >I am looking for a smiles to sdf converter able to run on PC/Win. Apparently >Babel might be the solution but the last version I could found for DO= S >environment (babel16) does not seem to support smiles among otherwise= wide >variety of input/output formats. > > > There is a more recent precompiled Windows version of Open Babel (successor to Babel) here: http://cml.sourceforge.net/new/ OpenBabel sort of supports SMILES but according to the docs it sets al= l the atom coordinates to zero instead of trying to build a reasonable 3= D geometry, so it may or may not fit your needs. -- Eric Bennett, Center for Drug Design, U of Minnesota -=3D This is automatically added to each message by the mailing script= =3D- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY)at(ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer= : Jan Labanowski, jlabanow)at(nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+ This e-mail, including any attachments, is a confidential business com= munication, and may contain information that is confidential, propriet= ary and/or privileged. This e-mail is intended only for the individua= l(s) to whom it is addressed, and may not be saved, copied, printed, d= isclosed or used by anyone else. If you are not the(an) intended reci= pient, please immediately delete this e-mail from your computer system= and notify the sender. Thank you. ------_=_NextPart_001_01C4D7EE.121A1C5A Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <= html xmlns:o=3D"urn:schemas-microsoft-com:office:office" xmlns:w=3D"ur= n:schemas-microsoft-com:office:word" xmlns:st1=3D"urn:schemas-microsof= t-com:office:smarttags" xmlns=3D"http://www.w3.org/TR/REC-html40">

C= ORINA will generate a 3D SD file from SMILES directly. There's a service, av= ailable on the web, that allow you to use CORINA in that way:

 

http://cactus.nci.nih.gov/services/translate=

 

Omar

 

_______________________

Omar Stradella

Computational Chemistry

Millennium Pharmaceuticals

40 La= ndsdowne St

<= font size=3D2 face=3D"Courier New">Cambridge, MA 021= 39

stradella)at(mpi.com

 

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net] = On Behalf Of Eric Bennett
Sent: Wednesday, December 01, 2004 2:09 PM
To: CHEMISTRY)at(ccl.net
Cc: Jiri Krechl
Subject: CCL:smiles to sdf converter

 

Jiri Krechl wrote:

 

>I am looking for a smiles to sdf converter able to run on = PC/Win. Apparently

>Babel might be the solution but the last version I could found for DOS<= /o:p>

>environment (babel16) does not seem to support smiles amon= g otherwise wide

>variety of input/output formats.<= /p>

> 

> 

> 

There is a more recent precompiled Windows version of Open Bab= el

(successor to Bab= el) here:

http://cml.sourceforge.net/new/

 

OpenBabel sort of supports SMILES but according to the docs it= sets all

the atom coordinates to zero instead of trying to build a reas= onable 3D

geometry, so it may or may not fit your needs.

 

--

Eric Bennett, Center for Drug Design, U of Minnesota

 

 

 

 

 

-=3D This is automatically added to each message by the mailin= g script =3D-

To send e-mail to subscribers of CCL put the string CCL: on yo= ur Subject: line

and send your message to:  CHEMISTRY)at(ccl.net

 

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net

HOME Page: http://www.ccl.net   | Jobs Page: http://= www.ccl.net/jobs

 

If your mail is bouncing from CCL.NET domain send it to the ma= intainer:

Jan Labanowski,  jlabanow)at(nd.edu (read about it on CCL Ho= me Page)

-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+

 

 

 

 

 




This e-mail, including any attachments, is a confidential business com=
munication, and may contain information that is confidential, propriet=
ary and/or privileged.  This e-mail is intended only for the individua=
l(s) to whom it is addressed, and may not be saved, copied, printed, d=
isclosed or used by anyone else.  If you are not the(an) intended reci=
pient, please immediately delete this e-mail from your computer system=
 and notify the sender.  Thank you.
------_=_NextPart_001_01C4D7EE.121A1C5A-- From chemistry-request@ccl.net Wed Dec 1 16:24:25 2004 Received: from castle.comp.uvic.ca (castle.comp.uvic.ca [142.104.5.97]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1LOMH9003748 for ; Wed, 1 Dec 2004 16:24:24 -0500 Received: from wm2.uvic.ca (ntsrvr5.comp.uvic.ca [142.104.5.65]) by castle.comp.uvic.ca (8.12.11/8.12.11) with ESMTP id iB1LdAlD5365892; Wed, 1 Dec 2004 13:39:10 -0800 X-WebMail-UserID: mdcooper Date: Wed, 1 Dec 2004 13:39:09 -0800 Sender: mdcooper From: mdcooper To: chemistry)at(ccl.net Cc: mdcooper)at(uvic.ca X-EXP32-SerialNo: 00003609 Subject: Mopac and Open Shells. Message-ID: <41AE5395)at(wm2.uvic.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.62 X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on castle X-UVic-Spam-Scan: castle.comp.uvic.ca Not_scanned_LOCAL X-Scanned-By: MIMEDefang 2.33 (www . roaringpenguin . com / mimedefang) X-Spam-Status: No, hits=2.2 required=7.5 tests=LINES_OF_YELLING, LINES_OF_YELLING_2,UPPERCASE_50_75 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I am trying to find the appropriate ionization potential for a single atom. I am using both C.I. and Open to declare an open shell and both of these commands give the expected HoF. What does happen, though, is that with C.I. the charge become 1, with OPEN the charge becomes -1 and with nothing the charge is the expected 0. Can someone help me figure out what is happening? Thanks, Matthew PM3 C.I.=(3,0) HEAT OF FORMATION = 170.890000 KCAL ELECTRONIC ENERGY = -111.229917 EV CORE-CORE REPULSION = .000000 EV DIPOLE = .00000 DEBYE NO. OF FILLED LEVELS = 1 AND NO. OF OPEN LEVELS = 1 CONFIGURATION INTERACTION WAS USED CHARGE ON SYSTEM = 1 IONIZATION POTENTIAL = 12.629698 EV PM3 OPEN(2,3) HEAT OF FORMATION = 170.890000 KCAL ELECTRONIC ENERGY = -111.229917 EV CORE-CORE REPULSION = .000000 EV DIPOLE = .00000 DEBYE NO. OF FILLED LEVELS = 1 AND NO. OF OPEN LEVELS = 3 CHARGE ON SYSTEM = -1 IONIZATION POTENTIAL = 2.956901 EV PM3 HEAT OF FORMATION = 231.554013 KCAL ELECTRONIC ENERGY = -108.599328 EV CORE-CORE REPULSION = .000000 EV DIPOLE = .00000 DEBYE NO. OF FILLED LEVELS = 2 IONIZATION POTENTIAL = 7.231552 EV From chemistry-request@ccl.net Wed Dec 1 16:24:36 2004 Received: from mx5.net.nih.gov (mx5.net.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB1LOXH9003801 for ; Wed, 1 Dec 2004 16:24:34 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id iB1LdLiQ015902 for ; Wed, 1 Dec 2004 16:39:21 -0500 Received: from AVAS.ncifcrf.gov ([129.43.27.170]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id iB1LdLQP015899; Wed, 1 Dec 2004 16:39:21 -0500 Received: from unknown(129.43.27.170) by AVAS.ncifcrf.gov via csmap id 93fb6e02_43e1_11d9_86d5_0002b3c7efe4_15708; Wed, 01 Dec 2004 16:40:11 -0500 (EST) Date: Wed, 1 Dec 2004 16:39:33 -0500 (Eastern Standard Time) From: "M. Nicklaus" To: Jiri Krechl cc: CHEMISTRY(at)ccl.net, mn1(at)helix.nih.gov Subject: Re: CCL:smiles to sdf converter In-Reply-To: <005401c4d7be$69a38a20$c964a8c0(at)spechem.cz> Message-ID: References: <005401c4d7be$69a38a20$c964a8c0(at)spechem.cz> X-X-Sender: mn1(at)helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Jiri, On Wed, 1 Dec 2004, Jiri Krechl wrote: > I am looking for a smiles to sdf converter able to run on PC/Win. Apparently > Babel might be the solution but the last version I could found for DOS > environment (babel16) does not seem to support smiles among otherwise wide > variety of input/output formats. If something that can be run *from* a PC instead of *on* one would be of use to you, you can use our web service at http://cactus.nci.nih.gov/services/translate/. You can submit text files with multiple SMILES strings, and you can choose between 2D and 3D coordinates in the generated SD file. Hope this helps, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1(at)helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design (CADD) Group Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------