From chemistry-request@server.ccl.net Thu Jan 11 02:47:18 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0B7lDp17208 for ; Thu, 11 Jan 2001 02:47:17 -0500 Received: from lmrmsm (202.127.25.5) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Thu, 11 Jan 2001 15:41:17 +0800 Message-ID: Comments: Authenticated sender is From: xmao@iris.sipp.ac.cn To: chemistry@ccl.net Date: Thu, 11 Jan 2001 15:38:30 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: question about the result of quantum chemistry literature databa Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Hello, everyone: I have a question about the result of Quantum Chemistry Literature DataBase ( at Japan), I want to consult the following article it gave me, but I can not find the vol 78 in 1991. ---------------- AU TACHIBANA A,ISHIZUKA N,YAMABE T JO THEODJ VO 74 PA 259 YE 91 --------------------- From the journal list of this database, the THEODJ is THEOCHEM(J. MOL.STRU.). I wish someone could help me find the real one. Thanks in advance. Regards, mao xiang From chemistry-request@server.ccl.net Thu Jan 11 04:29:16 2001 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0B9TGp17479 for ; Thu, 11 Jan 2001 04:29:16 -0500 Received: from chpc47.ch.unito.it (chpc47.ch.unito.it [130.192.118.47]) by silver.ch.unito.it (8.9.3/8.9.3) with SMTP id KAA26432; Thu, 11 Jan 2001 10:45:40 +0100 (MET) Message-Id: <3.0.3.32.20010111102551.007cd470@silver.ch.unito.it> X-Sender: teorica@silver.ch.unito.it X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Thu, 11 Jan 2001 10:25:51 +0100 To: Txema Mercero From: Theoretical Chemistry Group Subject: Re: CCL:[Fwd: II-VI materials] Cc: chemistry@server.ccl.net In-Reply-To: <3A5C6DEA.157049A8@sq.ehu.es> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 15.12 10/01/01 +0100, you wrote: >Txoni wrote: > > Hello! > > I'm interested on some information concerning II-VI materials, such > as ZnO, ZnS > and so on. I would like to know the values of cohesive energy of all > combinatioins, along > with the values of the atomic charges within the crystals. > > Thank you very much > > Txoni Matxain > PhD Student > See: http://www.ch.unito.it/ifm/teorica/elementi/node1.html#z30 Theoretical Chemistry Group University of Torino Via Giuria 5 - I 10125 Torino Italy Phone: +39 011 670 7564 Fax: +39 011 670 7855 E mail teorica@ch.unito.it From chemistry-request@server.ccl.net Thu Jan 11 04:46:17 2001 Received: from fjohn.Stanford.EDU (fjohn.Stanford.EDU [171.64.38.72]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0B9kHp17533 for ; Thu, 11 Jan 2001 04:46:17 -0500 Received: from localhost (greg@localhost) by fjohn.Stanford.EDU (8.9.3/8.9.3) with ESMTP id BAA14072 for ; Thu, 11 Jan 2001 01:46:17 -0800 Date: Thu, 11 Jan 2001 01:46:17 -0800 (PST) From: Greg Lakatos To: chemistry@ccl.net Subject: Correlation Functions in CHARMm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. Would anyone know the best way to calculate force-momentum cross correlation functions using CHARMm? In particular, is there a way to get CHARMm to produce a time series of the forces acting on each atom during a dynamics run, and then calculating the correlation function directly from this data? What I would like to avoid is taking the derivative of a velocity time series. Thank you for the assistance. - Greg Lakatos From chemistry-request@server.ccl.net Thu Jan 11 05:26:31 2001 Received: from mail2.zrz.tu-berlin.de (mail2.zrz.TU-Berlin.DE [130.149.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BAQVp17609 for ; Thu, 11 Jan 2001 05:26:31 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.21) id 14GewB-0007PL-00; Thu, 11 Jan 2001 11:26:31 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.21) id 14GewA-0004th-00; Thu, 11 Jan 2001 11:26:30 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <3A5CB37B.303B30D9@cornell.edu> References: <3A5CB37B.303B30D9@cornell.edu> Date: Thu, 11 Jan 2001 11:26:29 +0100 To: "Dr. Richard Wood" From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:document format for ACS journals? Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >I would think that given the wide availability of such programs, it >wouldn't matter >that a journal required such a thing. > As long as hard copies are accepted, everything is fine. Publishers simply have to concentrate on (quite few) electronic formats they feed to the production line, they are allowed to be restrictive there. If a publisher does not accept hard copies (only electronic versions), this becomes painful for those using non-standard word processors, and then it matters. Yours, -- +---------------------------------+-------------------------------------+ | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ From chemistry-request@server.ccl.net Thu Jan 11 03:21:58 2001 Received: from atol.icm.edu.pl (IDENT:root@atol.icm.edu.pl [212.87.0.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0B8Lrp17285 for ; Thu, 11 Jan 2001 03:21:53 -0500 Received: from burza.icm.edu.pl ([148.81.208.198]:32756 "EHLO burza.icm.edu.pl" ident: "IDENT-NONSENSE") by atol.icm.edu.pl with ESMTP id ; Thu, 11 Jan 2001 09:21:44 +0100 Received: (from lesyng@localhost) by burza.icm.edu.pl (8.9.3/8.9.3/rzm-2.6/icm) id JAA18445 for chemistry@ccl.net; Thu, 11 Jan 2001 09:21:26 +0100 (MET) Received: from burza.icm.edu.pl (burza.icm.edu.pl [148.81.208.198]) by burza.icm.edu.pl (8.9.3/8.9.3/rzm-2.6/icm) with SMTP id PAA22515; Tue, 9 Jan 2001 15:41:43 +0100 (MET) Message-Id: <200101091441.PAA22515@burza.icm.edu.pl> Date: Tue, 9 Jan 2001 15:41:43 +0100 (MET) From: Symposium on Inhibitors of Protein Kinases Reply-To: Symposium on Inhibitors of Protein Kinases Subject: 01.09.09 IPK2001 - Int. Conf. Inhibitors of Protein Kinases, Warsaw To: chemistry@ccl.net INVITATION TO PARTICIPATE IN THE IPK-2001 CONFERENCE ********************************************************************* IPK'2001: 2nd International Conference on INHIBITORS OF PROTEIN KINASES ********************************************************************* Design * Structural Biology * Phosphorylation/ Dephosphorylation Processes * Biochemistry * Biotechnology * Clinical Aspects * Chemotherapy Warsaw, Poland September 9 - 15, 2001 ORGANIZERS * ICM, University of Warsaw * Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAS) * Committee of Biochemistry & Biophysics, PAS * International Institute of Molecular & Cell Biology in Warsaw INVITATION The 1st International Conference on INHIBITORS OF PROTEIN KINASES (IPK'98), organized in Warsaw, Poland, September 15-20, 1998, was well received both by participants (see Pharmacology & Therapeutics 82 (Nos. 2-3), 1999), and the international scientific community. In the intervening two years, remarkable progress has been achieved in the development of highly specific inhibitors, their applications to delineation of cellular signaling pathways, and their potential for treatment of various pathological states. The 2nd such Conference, IPK'2001, to be held in Warsaw, September 9-15, 2001, is intended to provide up-to date knowledge and future perspectives, presented by leading specialists from both academia and the pharmaceutical industry, representing various disciplines from chemistry and biochemistry, through structural biology and drug design, to the clinic. In addition to invited lectures, ample opportunity will be provided for presentation of posters, some of which will be selected for oral presentation. Abstracts are to be submitted in accordance with the special Abstract Form available from the Conference Secretariat or through the Internet. Accepted abstracts will be published in a special number of the journal Cellular Mol. Biol. Lett. An additional feature of the program will be a Workshop on Molecular Modelling Techniques, with applications to protein kinases. Of interest to some participants may be the 8th Interbnational Symposium on ASPECTS of CHEMOTHERAPY, to be held in Gdansk, September 5-9, 2001 (see http://www.pg.gda.pl/Sympozja/mac.html), hence just prior to IPK'2001. INTERNATIONAL ADVISORY BOARD Dirk Bossemeyer (Germany) Philip Cohen (UK) William A. Denny (New Zealand) Yasuo Fukami (Japan) Brian A. Hemmings (Switzerland) Louise N. Johnson (UK) Edwin G. Krebs (USA) David S. Lawrence (USA) J. Andrew McCammon (USA) Alexander Levitzky (Israel) Eisuke Nishida (Japan) Lorenzo A. Pinna (Italy) Susan S. Taylor (USA) LOCAL ORGANIZING COMMITTEE David Shugar - Program Bogdan Lesyng - Organization Andrzej Rabczenko - Secretary Barbara Kleyny - Secretariat Grazyna Dobrowolska Nikodem Grankowski Teresa Jakubowicz Jacek Kuznicki Jan Maurin Malgorzata Mossakowska Grazyna Muszynska Maciej Nalecz CONFERENCE LANGUAGE: English For more information and preliminary registration see http://www.icm.edu.pl/ipk2001 E-mail address of the Conference secretariat is: ipk2001@icm.edu.pl. The attachement below contains the first announcement form in the MS Word format. [Removed from the message due to the size by jkl] From chemistry-request@server.ccl.net Thu Jan 11 04:00:01 2001 Received: from sirene.rz.uni-duesseldorf.de (sirene.rz.uni-duesseldorf.de [134.99.128.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0B900p17333 for ; Thu, 11 Jan 2001 04:00:00 -0500 Received: from koronium (koronium.ac2.uni-duesseldorf.de [134.99.76.30]) by neptun.rz.uni-duesseldorf.de (Sun Internet Mail Server sims.4.0.2000.05.17.04.13.p6) with SMTP id <0G6Z0080MQBY8G@neptun.rz.uni-duesseldorf.de> for chemistry@ccl.net; Thu, 11 Jan 2001 09:59:58 +0100 (MET) Date: Thu, 11 Jan 2001 10:11:16 +0100 From: Stefan Konietzny Subject: Summary: =?iso-8859-1?q?ECP=B4s=20and=20Basis=20Sets?= In-reply-to: <01010514402700.01598@koronium> To: chemistry@ccl.net Message-id: <01011110111600.00654@koronium> Organization: Institut =?iso-8859-1?q?f=FCr=20Anorganische=20Chemie=20und=20Strukturchemie?= MIME-version: 1.0 X-Mailer: KMail [version 1.1.99] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 8BIT References: <01010514402700.01598@koronium> Dear CCLers, thanks to Stefan Fau and Douglas Fox. Stefan´s reply went to the list, but not Douglas´. So, here it is. ************************* Dr. Konietzny, I have reproduced the problem of having a zero coefficient with the CEP-4G* designation actually applies to a number of elements where the standard polarization functions are not defined. Through Cl is fine but I am not aware of a generally acceptable set for the rest of the periodic table if they were not defined at the point the basis set was proposed in the literature. This is the case for the SDD basis sets. This is on the list for the developers but I will have to check on the status. There was an attempt to query the developers of the various ECP sets to see what work they had already done. You don't say it explicitly so let me make sure you are aware that you can augment the CEP-4G basis, or any of the others using the ExtraBasis keyword which lets you define polarization functions as needed. Thus specify the route as # HF/CEP-4G ExtraBasis supplying manual polarization functions 0 1 Bi 0.0 0.0 0.0 C 0.0 0.0 1.6 H 0.0 0.0 2.6 Bi 0 D 1 1.0 0.75 **** C 0 D 1 1.0 0.8 **** or you can mix/match # HF/Gen Pseudo=Read supplying manual polarization functions 0 1 Bi 0.0 0.0 0.0 C 0.0 0.0 1.6 H 0.0 0.0 2.6 Bi 0 SDD **** C H 0 6-31G* **** Bi 0 SDD where the second entry is for the core potential. GENECP is implemented in Rev. A.9 to combine GEN with PSEUDO=READ but the rest of the input is the same. I am sure you will get a lot of recommendations on how to optimize exponents. Since the d polarization functions will be formally empty you either need to use a correlated method or use an ECP where there are some occupied d orbitals before optimizing the d exponents will work. Both of these have been used, as you note, and while I would argue for MP2 atomic calculations as being a good approach which is relatively close-ended you may come to a different conclusion. Using different families of basis sets is also one where most of the variations have been tried. I would avoid using a minimum basis type of ECP and then pairing it with an extended basis set for the first and second row heavies for the same reason I would not suggest this with an all-electron basis, it tends to suffer from serious basis set superpostion error because deficiencies in the Bi valence basis will be solved by borrowing of basis functions from the rest of the molecule. Let me know if you need further assistance to help@gaussian.com. ************ From chemistry-request@server.ccl.net Thu Jan 11 04:47:11 2001 Received: from mail2.organik.uni-erlangen.de (lesath.chemie.uni-erlangen.de [131.188.127.212]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0B9lAp17544 for ; Thu, 11 Jan 2001 04:47:10 -0500 Received: from baal (baal [131.188.127.129]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with SMTP id KAA11811; Thu, 11 Jan 2001 10:47:05 +0100 (MET) From: Achim Herwig To: "Charlton, Michael" Subject: Re: CCL:viewing SDfiles Date: Thu, 11 Jan 2001 10:47:05 +0100 X-Mailer: KMail [version 1.1.99] Content-Type: text/plain; charset="iso-8859-1" References: <5FD8C12EECBBD4119DD10002B3027B9A023578@GABRIELLE> In-Reply-To: <5FD8C12EECBBD4119DD10002B3027B9A023578@GABRIELLE> Cc: chemistry@ccl.net MIME-Version: 1.0 Message-Id: <01011110470500.16441@baal> Content-Transfer-Encoding: 8bit Hi, a possibility (though I'm not sure about cheap for commercial applications) is the CACTVS system which covers all three of your problems and is even developed on a SGI (runs on other OSes, too): http://www2.ccc.uni-erlangen.de/software/cactvs/index.html HTH, Achim Herwig. Am Mittwoch, 10. Januar 2001 11:09 schrieben Sie: > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It > would be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) -- Achim Herwig | Achim.Herwig@chemie.uni-erlangen.de, achim@thc.mayn.de +49 9131 8526574 | http://www2.ccc.uni-erlangen.de/people/Achim_Herwig/ PGP-Fingerprint16 = 17 9A 42 C5 E8 72 A8 3F 96 27 7B A0 48 0B 88 F3 From chemistry-request@server.ccl.net Thu Jan 11 09:23:37 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0BEJXp18967 for ; Thu, 11 Jan 2001 09:21:34 -0500 Received: from iris.sipp.ac.cn (202.127.25.123) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Thu, 11 Jan 2001 22:21:12 +0800 Sender: user@ccl.net Message-ID: <3A5DC07A.7D8ADB93@iris.sipp.ac.cn> Date: Thu, 11 Jan 2001 22:17:30 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: summary bout the QCLD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello, everyone: I am sorry that I have a mistake in my email about the quantum chemistry literature data, it should be vol74, not vol78. I have received some replys about my problem. But I am still a little confused. I think Dr Borkent give the right volume number for THEODJ in our library, it is in the vol228 that I can got the article, but someone says that vol74 is right. I do not know why there is so big difference between vol74 and vol228. Thank you very much for all your reply. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Jan 11 12:25:24 2001 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BHPOp19384 for ; Thu, 11 Jan 2001 12:25:24 -0500 Received: (from serg@localhost) by markov.chem.rochester.edu (8.10.1/8.10.1) id f0CHPMi15457; Thu, 12 Jan 2001 12:25:22 -0500 (EST) Date: Thu, 12 Jan 2001 12:25:22 -0500 (EST) From: Sergei Tretiak To: "Ye, Sha Joshua" cc: "chemistry@ccl.net" Subject: Re: CCL:Polymer animations? In-Reply-To: <2F18332777@citrine.indstate.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Joshua, On MOLDEN homepage there are several recepies how to create aminations (http://www.cmbi.kun.nl/~schaft/molden/animations.html) using additional free software. But personally I do not think that this is the simplest way. If you need to create movies and manipulate with them (edit, merge, etc.) then commercial Adobe Premiere would be the way to go (however there are other commercial programs such as Apple Quick Time Pro which may similar capability). Best, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Theoretical Division | Voice: (505) 667-8351 | | Mail stop B262 | Fax: (505) 665-4063 | | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| On Wed, 10 Jan 2001, Ye, Sha Joshua wrote: > Dear Sergei, > What kind of software I can use to merge all GIFs into a movie > file? > Thanks in advance. > > Best regards, > Joshua > > > Date: Wed, 11 Jan 2001 15:39:28 -0500 > (EST) > > From: Sergei Tretiak > > To: kynn@panix.com > > Cc: "chemistry@ccl.net" > > Subject: CCL:Polymer animations? > > > Kevin, > > > > MOLDEN (http://www.cmbi.kun.nl/~schaft/molden/molden.html) will do the > > job for you. It can generate graphics GIF files for each step and play it > > like a movie, but to merge all GIFs into a single movie file you have to > > use another software. > > > > Best, > > > > Sergei > > > > >.-----------------------------------------------------------------------. > > |\ / \ | Sergei Tretiak | / \ /| > > |.\/...\|.......................................................|/...\/.| > > | Theoretical Division | Voice: (505) 667-8351 | > > | Mail stop B262 | Fax: (505) 665-4063 | > > | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | > > | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | > > | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | > > |_______________________________________________________________________| > > > > > > On Wed, 10 Jan 2001 kynn@panix.com wrote: > > > > > > > > > > > > > > > > > Hi. I've written a program to simulate the behavior of short, linear > > > polymer under the influence of a specialized force field I developed. > > > The program can easily produce a list of coordinates for all the > > > monomers along the chain at periodic time intervals during a > > > simulation. I would like this information to make a movie of the > > > polymer in action under this force field. Therefore, I'm looking for > > > a simple, public-domain piece of software that I can feed these > > > coordinates to, and will generate the corresponding graphics and play > > > them back as a movie. > > > > > > Any suggestions? > > > > > > Thanks! > > > > > > Kevin > > > > > > > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > Sha Joshua Ye > 200 Farrington St. > Apt408 > Terre Haute,IN 47807 > Tel:812-237-7338(h),812-237-8704(o) > Email:joshua_ye@yahoo.com ;yes@citrine.indstate.edu > From chemistry-request@server.ccl.net Thu Jan 11 09:16:06 2001 Received: from matavnet.hu (mail.matavnet.hu [195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0BEG5p18955 for ; Thu, 11 Jan 2001 09:16:06 -0500 Received: (qmail 1632 invoked from network); 11 Jan 2001 10:48:24 +0100 Received: from line-127-225.dial.matav.net (HELO chemaxon.com) (145.236.127.225) by mail.matavnet.hu with SMTP; 11 Jan 2001 10:48:24 +0100 Message-ID: <3A5D7E8A.8A90D6A5@chemaxon.com> Date: Thu, 11 Jan 2001 10:36:11 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Daniel Severance CC: chemistry@ccl.net Subject: Re: CCL:Viewing multiple structure files References: <15189A4705A8D31189B700805F85410B41436C@sdnt1> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Daniel, What do you mean by scrolling through the conformations? - Should they appear side by side in different cells of a table? In this case you may apply MarvinView's table display option - Or should they be displayed one after the other in one cell. You can create an HTML page consisting MarvinView applet, which loads the files consecutively using a custom function that calls the windows.timeOut(...) method. MarvinView's Edit | Source popup menu option enables the chemists to retrieve file in several formats, like Molfile and Smiles. 3D rotation is supported. If you need more information or help, please contact me. Regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com mailto:fcsiz@chemaxon.com Daniel Severance wrote: > Greetings CClers, > I've generated a set of conformations of a molecule and want to send it > to some chemists at a remote site. > Is there a simple application (Windows NT) for simply scrolling through the > set of conformations one at > a time (visually, with 3D rotation ability) so they can see the results? It > needs to do nothing else, although it > might be nice to be able to dump out the current conformation into a new > file, it wouldn't be required. > Is there anything available to do this (either academic or commercial is > fine)? > Thanks! > Dan > > ____________________________________________________ > Daniel L. Severance Ph.D. > Computational Chemistry > ACADIA Pharmaceuticals > 3911 Sorrento Valley Boulevard > San Diego CA 92121-1402 USA > > phone (858) 558 2871 > fax (858) 558 2872 > dseverance@acadia-pharm.com > www.acadia-pharm.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jan 11 09:54:00 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BEs0p19053 for ; Thu, 11 Jan 2001 09:54:00 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA14203 for ; Thu, 11 Jan 2001 09:54:00 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A5DC833.A8964596@cornell.edu> Date: Thu, 11 Jan 2001 09:50:27 -0500 From: "Dr. Richard Wood" Organization: Cornell University 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: Re: CCL:document format for ACS journals? References: <20010110082456.A695@hpotter.vaughan.home> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Kenward Vaughan wrote: > Personally I would be very troubled if an organization such as the ACS > decreed that submissions were dependent on specific software rather than > styles. Certainly that group knows the great strengths which lie in other, > well-established software available to the academic community, especially > since it is (literally) free _and_ created in the spirit of the academic > world? > > Perhaps they need to revamp their "document-handlers" pool... Or perhaps we need to be not so serious? People make it seem like nobody in the world uses MS Word or Word Perfect, or that it is impossible to get either. While I was still a graduate student (without funding, btw) I was able to purchase my OWN copy of MS Word (which I composed my dissertation on); and we all know that researchers in academe NEVER pay for software out of their own pockets, plus they generally get an academic discount, the same with textbooks. So what is the big deal here? > Kenward Vaughan > Bakerfield College > kvaughan@bc.cc.ca.us (work) Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Jan 11 09:58:38 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BEwcp19068 for ; Thu, 11 Jan 2001 09:58:38 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA22946 for ; Thu, 11 Jan 2001 09:58:38 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A5DC949.89973799@cornell.edu> Date: Thu, 11 Jan 2001 09:55:05 -0500 From: "Dr. Richard Wood" Organization: Cornell University 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: Re: CCL:document format for ACS journals? References: <3A5CB37B.303B30D9@cornell.edu> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Christoph van Wüllen wrote: > >I would think that given the wide availability of such programs, it > >wouldn't matter > >that a journal required such a thing. > > > > As long as hard copies are accepted, everything is fine. Publishers simply > have to concentrate on (quite few) electronic formats they feed to > the production line, they are allowed to be restrictive there. > > If a publisher does not accept hard copies (only electronic versions), this > becomes painful for those using non-standard word processors, and > then it matters. > Then isn't that the problem/fault of the individual and NOT the journal? I mean it's not the ACS's fault if one chooses to not use a program such as MS Word which can be EASILY obtained. There are things far more serious that we should be getting worked up about. > Yours, > > -- > +---------------------------------+-------------------------------------+ > | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | > | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | > | Strasse des 17. Juni 135 | eMail | > | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | > +---------------------------------+-------------------------------------+ Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Jan 11 10:56:14 2001 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BFuDp19186 for ; Thu, 11 Jan 2001 10:56:13 -0500 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id HAA15826 for ; Thu, 11 Jan 2001 07:57:57 -0800 (PST) Received: from 40dhcp46.msi.com(146.202.40.198) by mailhost.msi.com via smap (V2.0) id xma015816; Thu, 11 Jan 01 07:57:40 -0800 Received: by localhost with Microsoft MAPI; Thu, 11 Jan 2001 08:06:13 -0800 Message-ID: <01C07BA5.5D69A9C0.johnw@msi.com> From: John Wintersteen Reply-To: "johnw@msi.com" To: "'CHEMISTRY@ccl.net'" Subject: RE: CCL:viewing SDfiles Date: Thu, 11 Jan 2001 08:06:11 -0800 Organization: Molecular Simulations Inc. X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit In reading Michael Charlton's message I thought it might be helpful to point out that in MSI's WebLab Viewers, there are is an alternate view, called the Hierarchy Window that provides a tool for viewing molecules one at a time in a multiple molecule file. The Hierarchy window will present a list of the molecules in the file. The Hierarchy Window and the 3D Window are presented side-by-side. While in the Hierarchy Window, using the Display Tool, you can show/hide molecules individually or in groups. Once the Display Tool has been engaged, you can also use the up and down arrows keys to scroll through the list of molecules. For files containing only a few molecules, the Tile Molecules in Window Command can be used to automatically space out the molecules in the 3D Window. The WebLab Viewer also has exporters for writing out image files in several file formats including gif, jpeg, and bmp. Regards, John Wintersteen Product Manager, Experimental Chemistry Molecular Simulations Inc. >From: "Charlton, Michael" >To: "'CHEMISTRY@ccl.net'" >Subject: CCL:viewing SDfiles >Date: Wed, 10 Jan 2001 15:31:59 -0000 >X-Mailer: Internet Mail Service (5.5.2650.21) >Sender: "Computational Chemistry List" > >Many thanks for all the replies (below) I received. >I feel I ought to clarify what I want here. >I can view structures in SDfiles already, using typical modelling packages >(MOE, Cerius etc.), but I am after a program that will allow lots of >chemists to browse them (hence the requirement for cheapness). The idea is >to be able to flick up and down, one at a time, or perhaps several >structures tiled on a page at a time. The pssmiles utility that comes with >with ClogP does this kind of thing, except postscript output is not very >convenient. >A common proposed solution is MSI's weblab viewer. However, whenever I open >an SDfile, I get all the structures overlaid on one another - 3000 >structures looks like a pile of spaghetti!! I have yet to find a use for >this - has anyone else ? ;-) >The program I dream of could be stand-alone (for distribution around company >PCs) or web-based (my intranet pages are on an SGI, so the clever bits would >need to be on that). My preference would be for 2D Isis Draw/ ChemDraw >style output rather than 3D, since most of the structures are only 2D. >My (sadly lacking) web skills could probably patch in a "smiles-to-gif" >utility to do what I want, if such a thing existed. Whilst I have been >composing this, a message from Marc Nicklaus just came in, and this could be >what I am after for the gif generation. > >Thanks again, > >Michael Charlton. >Replies : >Michael, > From chemistry-request@server.ccl.net Thu Jan 11 11:42:26 2001 Received: from sol.cc.u-szeged.hu (root@[160.114.8.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BGgPp19290 for ; Thu, 11 Jan 2001 11:42:25 -0500 Received: from fk01 by sol.cc.u-szeged.hu (8.9.3+Sun/SMI-SVR4) id RAA27770; Thu, 11 Jan 2001 17:42:08 +0100 (MET) From: "Zoltan A. Fekete" Organization: University of Szeged To: Christoph van Wüllen Date: Thu, 11 Jan 2001 17:42:07 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-2 Subject: Re: CCL:document format for ACS journals? CC: chemistry@ccl.net Message-ID: <3A5DF06F.5319.66AB74A@localhost> Priority: normal In-reply-to: References: <3A5CB37B.303B30D9@cornell.edu> X-mailer: Pegasus Mail for Win32 (v3.12c) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id f0BGgQp19291 On 11 Jan 2001, at 11:26, Christoph van Wüllen wrote: >[...] If a publisher does not accept hard copies (only electronic versions), this > becomes painful for those using non-standard word processors, and > then it matters. But we should WANT the publishers to require electronic versions, in order for them to provide us with publications available in true electronical format (rather than makeshift copies like graphic-only PDF scan some journals have these days)! And for that it is better to ask those using non-standard word processors to have their format converted into something widely accessible, than to expect all the world to have converters for everybody else's particular piece of software... Dr. Zoltan A. Fekete SZTE University of Szeged, Department of Physical Chemistry Szeged, Rerrich ter 1, POB 105, H-6701 Hungary, FAX 36-62-544652 From chemistry-request@server.ccl.net Thu Jan 11 12:05:37 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BH5bp19331 for ; Thu, 11 Jan 2001 12:05:37 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id MAA25737; Thu, 11 Jan 2001 12:05:33 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 11 Jan 2001 12:05:29 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G70009GNCMZ92@lvlmail.unitedcatalysts.com>; Thu, 11 Jan 2001 12:01:47 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 11 Jan 2001 12:04:48 -0500 Content-return: allowed Date: Thu, 11 Jan 2001 12:04:47 -0500 From: "Shobe, Dave" Subject: RE: summary bout the QCLD To: "'Mao Xiang'" , "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAABBD@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 f0BH5bp19332 I've seen Theochem numbered in two ways. One is as part of J. Mol. Struct., the other is as its own journal. FWIW, Elsevier uses the J. Mol. Struct. numbering on its web site and in its contents direct service. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com -----Original Message----- From: Mao Xiang [mailto:xmao@iris.sipp.ac.cn] Sent: Thursday, January 11, 2001 9:18 AM To: chemistry@ccl.net Subject: CCL:summary bout the QCLD hello, everyone: I am sorry that I have a mistake in my email about the quantum chemistry literature data, it should be vol74, not vol78. I have received some replys about my problem. But I am still a little confused. I think Dr Borkent give the right volume number for THEODJ in our library, it is in the vol228 that I can got the article, but someone says that vol74 is right. I do not know why there is so big difference between vol74 and vol228. Thank you very much for all your reply. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Jan 11 13:11:07 2001 Received: from myrtle.rtpnc.epa.gov (myrtle.rtpnc.epa.gov [134.67.208.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BIB7p19490 for ; Thu, 11 Jan 2001 13:11:07 -0500 Received: from epahub11.rtp.epa.gov (epahub11.rtp.epa.gov [134.67.213.52]) by epamail.epa.gov (PMDF V5.2-32 #42055) with ESMTP id <0G7000G9JFJJ11@epamail.epa.gov> for chemistry@ccl.net; Thu, 11 Jan 2001 13:04:32 -0500 (EST) Date: Thu, 11 Jan 2001 13:04:25 -0500 From: Moudgal.Chandrika@epamail.epa.gov Subject: questions---------- To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Content-type: text/plain; charset=iso-8859-1 X-MIMETrack: Serialize by Router on EPAHUB11/USEPA/US(Release 5.0.5 |September 22, 2000) at 01/11/2001 01:04:30 PM Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f0BIB7p19491 Hello All, I have a three questions I need help with. 1) A couple of my associates and I are currently in the process of developing a QSTR model capable of predicting quantitative estimates for carcinogenic potency. We have come across a few citations on such work, but nothing concrete. Could you please provide us with more references, information on any existing models, or give suggestions as to how we may proceed. 2) We are also interested in developing models capable of predicting mechanism of action, particularly via the p450 enzyme class. I know some work has been done in this area, but not very extensive. If we can get more information on this topic, we would greatly appreciate it. 3) I am also looking for more information on the "Computational Methods in Toxicology" workshop that was held in Dayton, Ohio in April 1998. In particular, I am interested in a presentation titled "Expert computer systems for toxicity and metabolism prediction" by Dr. Nigel Greene. If this presenter is listed on the CCL Listserv, a message from you would be much appreciated. 4) We are looking to send several employees to a well organized QSAR/QSTR training course. Are there any such training courses available in the North American Continent? Our emphasis is mainly in QSAR / QSTR modeling which will aid us in predicting human health related endpoints and augment the risk assessment process. Thank you all in advance for your responses. E-mail address can be found at the bottom of this message. Chandrika Chandrika J. Moudgal National Center for Environmental Assessment, US EPA 26 W. Martin Luther King Dr., ML 117 Cincinnati, OH 45268 Phone: 513-569-7078 Fax: 513-569-7475 e-mail: moudgal.chandrika@epa.gov From chemistry-request@server.ccl.net Thu Jan 11 18:02:26 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BN2Qp20551 for ; Thu, 11 Jan 2001 18:02:26 -0500 Received: from gothos.ccl.net (gothos.ccl.net [192.148.249.204]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id SAA05571; Thu, 11 Jan 2001 18:02:25 -0500 (EST) Date: Thu, 11 Jan 2001 18:02:24 -0500 From: Scott Brozell To: chemistry@ccl.net, journals@acs.org Subject: Re: CCL:document format for ACS journals? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, TeX is widely used in the scientific world for document preparation. For example, The American Mathematical Society and The American Physical Society provide TeX templates for abstract and manuscript submission. http://www.ams.org/jourhtml/latexbenefits.html http://publish.aps.org/esubs/guidelines.html#fileformat TeX is exquisite. TeX is free. The TeX programs are bugless. http://www.tug.org/ I strongly encourage the ACS to support TeX document preparation. Scott Brozell, Ph.D. Ohio SuperComputer Center On Wed, 10 Jan 2001, David van der Spoel wrote: > On Wed, 10 Jan 2001, Dr. Martin Schuetz wrote: > > On Wed, 10 Jan 2001, Stefan Grimme wrote: > > > Dear CCl users, > > > In my opinion we all should ignore the publishers requests > > > for articles in special formats, mostly commercial (MS). I don't like to be > > > forced to use this software and if they don't accept formats I'm using (LaTeX), > > > I will not consider these journals anymore. > >I agree totally. One might even consider to go one step further and to > >refuse any reviewing tasks for ACS journals... > Not so fast... > > According to the JPC website one can send in papers in a stripped down > Latex, i.e., things like bold, math etc. are preserved, which is what > counts. > > But a boycot of Nature would be in place... They can't even print an EPS > file. From chemistry-request@server.ccl.net Thu Jan 11 18:30:46 2001 Received: from bnpi.com (bnpi.com [208.188.148.225] (may be forged)) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0BNUkp20672 for ; Thu, 11 Jan 2001 18:30:46 -0500 Received: from BNPISRV2 by bnpi.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 11 Jan 2001 23:37:11 UT Received: from bnpi.com (b27 [198.213.32.6]) by bnpisrv2.bnpi.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id CRPTYMLZ; Thu, 11 Jan 2001 17:26:13 -0600 Sender: jeff@ccl.net Message-ID: <3A5E41AE.F460AFFB@bnpi.com> Date: Thu, 11 Jan 2001 17:28:46 -0600 From: Jeff Saxe X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Curves5.3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Last month one of my colleagues got the Curves5.3 program. When I checked this program I discovered that in the eigen subroutine there is a variable, mv, which is used, however this variable has never been defined. I wrote to Richard Lavery to ask about this, but have not yet received a reply. Has anyone else looked into this to determine what mv should be, or does anyone have a version of this program which does have mv defined? Thank you for any help. Jeff -- Jeffrey D. Saxe BioNumerik Pharmaceuticals, Inc. Suite 400, 8122 Datapoint Dr., San Antonio, TX 78229 email jeff.saxe@bnpi.com phone 210-614-1701 x225 fax 210-614-2892 From chemistry-request@server.ccl.net Thu Jan 11 16:36:59 2001 Received: from hotmail.com (f250.law4.hotmail.com [216.33.148.128]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BLaxp20291 for ; Thu, 11 Jan 2001 16:36:59 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 11 Jan 2001 13:35:00 -0800 Received: from 128.101.135.68 by lw4fd.law4.hotmail.msn.com with HTTP; Thu, 11 Jan 2001 21:35:00 GMT X-Originating-IP: [128.101.135.68] From: "Wen Qiu" To: chemistry@ccl.net Cc: ymo@chem.umn.edu Subject: ionic interaction in biosystems Date: Thu, 11 Jan 2001 21:35:00 -0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 11 Jan 2001 21:35:00.0644 (UTC) FILETIME=[59F09E40:01C07C16] Dear CCL's, Could someone provide me with references or leads in literature that has reported the strength of salt-bridges or ionic interactions mimicing situations in biological systems. For example, what is the binding/interaction energy for R-CH2-COO(H)...(H3)N-R (where R is any alkyl group) or aspartate/glutamate...lysine/arginine I am more interesed in ab initio results and also the sensitivity of these calculations with respect to the choice of ab initio methods and basis sets. I will also be interested in knowing about reported experimental figures for this and related systems. If there is sufficient interest, I will summarize the replies to CCL. Cheers, Wen Qiu _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com From chemistry-request@server.ccl.net Thu Jan 11 17:39:35 2001 Received: from jaguar.it.wsu.edu (root@jaguar.it.wsu.edu [134.121.0.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BMdZp20452 for ; Thu, 11 Jan 2001 17:39:35 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id OAA11298; Thu, 11 Jan 2001 14:21:39 -0800 (PST) Message-ID: <002901c07c1c$dd61b330$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: Cc: , References: <862569D0.005BE894.00@unomail.unomaha.edu> Subject: Re: CCL:Quick question on G98 Date: Thu, 11 Jan 2001 14:21:37 -0800 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello Dr. Stack, I believe the answer to your question is yes. Doug Fox at Gaussian, Inc. clued me into this when I was having trouble with a dual-cpu system running in Linux. I do not know how to change the shmem variable in IRIX as my experience is mostly limited to linux and windows systems. In linux (if it helps...) one can change the shmem by su'ing and typing the following: echo "536870912" >/proc/sys/kernel/shmmax this would set the shmem variable to 512MB. Also, I would like to mention that I incorrectly referred to NUMA and UMA previously when I should have been referring to distributed (instead of NUMA) versus shared (instead of UMA) memory systems. Credit goes to Jim Phillips for bringing this to my attention and "adjusting" my views on this matter. Thank you Jim. Since Doug Fox helped me with shmem in linux I would hit him up specifically for help on this. Respectfully, Phillip Matz matz@wsunix.wsu ----- Original Message ----- From: To: "Phillip D. Matz" Cc: ; Sent: Wednesday, January 10, 2001 8:43 AM Subject: CCL:Quick question on G98 > Dear Phillip, > > > Thanks again for your clear insight. Is there another issue to consider, namely > the shmem variable. Isn't a Unix kernel compiled to set the maximum amount of > memory one processor can use. I refer specifically to an SGI Orgin 2000 running > IRIX 6.5. How does one change this value (I think many default to 512 MB). > > Thanks again! > > Douglas E. Stack > Assistant Professor > Department of Chemistry > University of Nebraska at Omaha > Omaha, NE 68182-0109 > (402) 554-3647 > (402) 554-3888 (fax) > destack@unomaha.edu > > From chemistry-request@server.ccl.net Thu Jan 11 18:06:52 2001 Received: from localhost.ox.ac.uk (root@[163.1.16.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0BN6pp20606 for ; Thu, 11 Jan 2001 18:06:51 -0500 Received: from smplinux.de (marc@localhost [127.0.0.1]) by localhost.ox.ac.uk (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id WAA08661 for ; Thu, 11 Jan 2001 22:28:47 GMT Message-Id: <200101112228.WAA08661@localhost.ox.ac.uk> X-Authentication-Warning: localhost.ox.ac.uk: Host marc@localhost [127.0.0.1] claimed to be smplinux.de X-Mailer: exmh version 2.1.1 10/15/1999 (debian) To: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? In-reply-to: Your message of "Thu, 11 Jan 2001 09:55:05 EST." <3A5DC949.89973799@cornell.edu> X-url: X-face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 11 Jan 2001 22:28:47 +0000 From: Marc Baaden Hello there, in general I don't interfere too much with the discussions on the list, but I must say, that I strongly disagree with the latest posts on this subject, and I would like to make an important point (at least in my opinion): Isn't the (MOST) important thing about publishing a scientific article the content of the article ? At least I thought so .. ? In that sense I suggest that NO ONE should be "discriminated" because he doesn't use MS Word. And let me add that I know a number of well-established groups where you wouldn't find a single copy of MS Word, and still they publish excellent articles in excellent journals. Isn't the job of the scientist to do actual research and then share this knowledge with thescientific community ? Even if the article was hand-written, it could be a Nobel prize, no ? So, well I certainly exaggerate, but I hope my point is clear. Let me just add that furthermore a scientist's job (even not for a computer scientist) is NOT to do typesetting, conversion of file- formats etc., ... This is the editor's job. That's what he should actually be doing. And so I pledge that an article, presented in any carefully written form should ALWAYS be considered for publication, whether it is in a convenient file format or not. A last general point is, that even using MS word exclusively, you have to spend a lot of time on getting a document which meets some of the file format guidelines given on several Journal webpages. That is, you particularly run in trouble if the article is written jointly by several groups and they use different versions of Word (Word 6, Word 97, Word 2000, Word for Mac, ...). For some PC documents for example it is IMPOSSIBLE to open them on a Mac .... Imposing thus a fixed file format/version would imply buying a new computer, changing the operating system, changing the program version ... ?? (Again I exaggerate, though I have painful experience with spending up to two weeks just for producing a coherent file format for some papers ..) I'd also like to make some specific comments: fekete@chem.u-szeged.hu said: >> But we should WANT the publishers to require electronic versions, in >> order for them to provide us with publications available in true >> electronical format (rather than makeshift copies like graphic-only >> PDF scan some journals have these days)! You wouldn't solve that problem by imposing a fixed file format.The journals producing such PDF files in general require camera ready formats, because they don't want to spend ANY time on re-typing/reprocessing your document, even not if it is in Word format. Furthermore, MS Word is not really a good format for what you suggest. You'd rather need a format like XML for example, where the output "medium" can easily be modified (html/pdf/ps/...) without touching the contents. fekete@chem.u-szeged.hu said: >> And for that it is better to ask those using non-standard word >> processors to have their format converted into something widely >> accessible, than to expect all the world to have converters for >> everybody else's particular piece of software... Sorry, but I really cannot agree with that. First, on what basis do you claim that MS Word would be something widely accessible and preferrable to for example LaTex ? Second, I wouldn't expect anybody to have any converter. Either the publisher/editor should do his work and really typeset the manuscript, starting from scratch, or even if they do it electronically, a simple ASCII text file might be of as much help as a Word document (again I exagerate, but what I want to make clear is that except [maybe] the spacing and the font characteristics like plain/bold/etc., the editor anyway doesn't need any further information. The tables are ALWAYS re-done,and the figures are also inserted separately. rlw28@cornell.edu said: >> Or perhaps we need to be not so serious? People make it seem like >> nobody in the world uses MS Word or Word Perfect, or that it is >> impossible to get either. While I was still a graduate student >> (without funding, btw) I was able to purchase my OWN copy of MS Word >> (which I composed my dissertation on); and we all know that >> researchers in academe NEVER pay for software out of their own >> pockets, plus they generally get an academic discount, the same with >> textbooks. >> So what is the big deal here? The deal is, that you wouldn't want to waste your time to migrate all your working environment set up for years to a system as restricted and unreliable as windows, nor loose your nerves trying to convert to any imposed format. In particular as it's the CONTENT of the article that s important and not it's design ! rlw28@cornell.edu said: >> > If a publisher does not accept hard copies (only electronic >> > versions), this becomes painful for those using non-standard word >> > processors, and then it matters. >> Then isn't that the problem/fault of the individual and NOT the >> journal? I mean it's not the ACS's fault if one chooses to not use a >> program such as MS Word which can be EASILY obtained. No, definitely not ! The individual is called a scientist, and his task is to do research, as good as he can. And if that includes not using MS Windows per default, than it's the scientist's choice, but it in no way lessens the value of the research that was performed. Imposing a file format is just an obstacle and a subjective way of selecting research not by its quality, but by a "commercial" criterion. Best regards, Marc Baaden -- Dr. Marc Baaden - Labo MSM (UMR 7551) - http://crypt.u-strasbg.fr/marc mailto:baaden@chimie.u-strasbg.fr - FAX (+49) 40 33 39 68 50 8 ICQ# 11466242 - Tel: (+33) 6 09 84 32 17 or (+49) 40 33 39 68 50 8 From chemistry-request@server.ccl.net Thu Jan 11 19:14:05 2001 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0C0E5p21023 for ; Thu, 11 Jan 2001 19:14:05 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id TAA06435; Thu, 11 Jan 2001 19:14:04 -0500 (EST) Date: Thu, 11 Jan 2001 19:14:04 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: jkl@ccl.net Subject: Re: CCL:document format for ACS journals? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers, I hope that it may be time to put the ACS journal format discussion to the grave... As long as they accept paper papers, it is OK. A paper is a paper... And you know what you can do with most of them... [hint: read {:-)}]. When they say "No to traditional paper", we will have a problem... At least me... I love paper books and paper papers... Maybe by the time the publishers say no to paper, we will be publishing everything in XML and each publisher will make the detailed DTD or schema. It will be a nightmare with all these incompatible document types, but it will be word processor independent, unless we will be forced to accept MicroSoft proprietary extensions... Of course, each publisher will have its own set of rules and tags. For example, there is little hope that people will ever agree on a standard for literature citations {:-)} and chemists (for sure) will reject any effort to standardize the format of molecular geometry file... So... Please... Let us go on with chemistry... Jan jkl@ccl.net P.S. We are moving CCL.NET to a new room, to new computers and a new Linux kernel... You probably noticed that some things do not work... Let us hope that they will, one day... We even incurred a disk crush in the process (on our main mail server). Thank you for your donations which help us to get new computers and parts (though the OSC generosity is in most part responsible for this...). Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Thu Jan 11 19:35:01 2001 Received: from argyle.richmond.edu (argyle.richmond.edu [141.166.188.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0C0Z1p21106 for ; Thu, 11 Jan 2001 19:35:01 -0500 Received: from sabrash (ppp065171.richmond.edu [141.166.65.171]) by argyle.richmond.edu (8.11.0/8.11.0) with SMTP id f0C0YwB15403; Thu, 11 Jan 2001 19:34:58 -0500 (EST) Message-Id: <3.0.5.32.20010111193300.00829180@facstaff.richmond.edu> X-Sender: sabrash@facstaff.richmond.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 11 Jan 2001 19:33:00 -0500 To: Marc Baaden , chemistry@ccl.net From: "Samuel A. Abrash" Subject: Re: CCL:document format for ACS journals? In-Reply-To: <200101112228.WAA08661@localhost.ox.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Marc, and the majority of correspondents on this issue. An early post quoted the ACS style guide. The post clearly stated that the factual basis of this thread is incorrect. ACS accepts word processors other than Word and Wordperfect. In fact, as long as the document is clearly labelled with word processor and computer, they will accept any word processor, including TEX and LATEX. It is time that we ended a thread made pointless by its response to an initial incorrect assertion. Samuel A. Abrash At 10:28 PM 01/11/2001 +0000, Marc Baaden wrote: > >Hello there, > >in general I don't interfere too much with the discussions >on the list, but I must say, that I strongly disagree with >the latest posts on this subject, and I would like to make >an important point (at least in my opinion): > >Isn't the (MOST) important thing about publishing a scientific >article the content of the article ? At least I thought so .. ? > >In that sense I suggest that NO ONE should be "discriminated" >because he doesn't use MS Word. And let me add that I know a >number of well-established groups where you wouldn't find a >single copy of MS Word, and still they publish excellent articles >in excellent journals. > > >Isn't the job of the scientist to do actual research and then >share this knowledge with thescientific community ? > >Even if the article was hand-written, it could be a Nobel prize, >no ? > >So, well I certainly exaggerate, but I hope my point is clear. > > >Let me just add that furthermore a scientist's job (even not for a >computer scientist) is NOT to do typesetting, conversion of file- >formats etc., ... > >This is the editor's job. That's what he should actually be doing. >And so I pledge that an article, presented in any carefully written >form should ALWAYS be considered for publication, whether it is in >a convenient file format or not. > > >A last general point is, that even using MS word exclusively, you have >to spend a lot of time on getting a document which meets some of the >file format guidelines given on several Journal webpages. That is, you >particularly run in trouble if the article is written jointly by several >groups and they use different versions of Word (Word 6, Word 97, Word 2000, >Word for Mac, ...). For some PC documents for example it is IMPOSSIBLE to >open them on a Mac .... >Imposing thus a fixed file format/version would imply buying a new computer, >changing the operating system, changing the program version ... ?? >(Again I exaggerate, though I have painful experience with spending up to >two weeks just for producing a coherent file format for some papers ..) > > >I'd also like to make some specific comments: > > >fekete@chem.u-szeged.hu said: >>> But we should WANT the publishers to require electronic versions, in >>> order for them to provide us with publications available in true >>> electronical format (rather than makeshift copies like graphic-only >>> PDF scan some journals have these days)! > >You wouldn't solve that problem by imposing a fixed file format.The journals >producing such PDF files in general require camera ready formats, because >they don't want to spend ANY time on re-typing/reprocessing your document, >even not if it is in Word format. >Furthermore, MS Word is not really a good format for what you suggest. You'd >rather need a format like XML for example, where the output "medium" >can easily be modified (html/pdf/ps/...) without touching the contents. > > >fekete@chem.u-szeged.hu said: >>> And for that it is better to ask those using non-standard word >>> processors to have their format converted into something widely >>> accessible, than to expect all the world to have converters for >>> everybody else's particular piece of software... > >Sorry, but I really cannot agree with that. First, on what basis do you >claim that MS Word would be something widely accessible and preferrable >to for example LaTex ? >Second, I wouldn't expect anybody to have any converter. Either the >publisher/editor should do his work and really typeset the manuscript, >starting from scratch, or even if they do it electronically, a simple >ASCII text file might be of as much help as a Word document (again I >exagerate, but what I want to make clear is that except [maybe] the >spacing and the font characteristics like plain/bold/etc., the editor >anyway doesn't need any further information. >The tables are ALWAYS re-done,and the figures are also inserted separately. > > > >rlw28@cornell.edu said: >>> Or perhaps we need to be not so serious? People make it seem like >>> nobody in the world uses MS Word or Word Perfect, or that it is >>> impossible to get either. While I was still a graduate student >>> (without funding, btw) I was able to purchase my OWN copy of MS Word >>> (which I composed my dissertation on); and we all know that >>> researchers in academe NEVER pay for software out of their own >>> pockets, plus they generally get an academic discount, the same with >>> textbooks. >>> So what is the big deal here? > >The deal is, that you wouldn't want to waste your time to migrate all >your working environment set up for years to a system as restricted and >unreliable as windows, nor loose your nerves trying to convert to any >imposed format. In particular as it's the CONTENT of the article that s >important and not it's design ! > > > >rlw28@cornell.edu said: >>> > If a publisher does not accept hard copies (only electronic >>> > versions), this becomes painful for those using non-standard word >>> > processors, and then it matters. >>> Then isn't that the problem/fault of the individual and NOT the >>> journal? I mean it's not the ACS's fault if one chooses to not use a >>> program such as MS Word which can be EASILY obtained. > >No, definitely not ! The individual is called a scientist, and his task >is to do research, as good as he can. And if that includes not using >MS Windows per default, than it's the scientist's choice, but it in no >way lessens the value of the research that was performed. Imposing a file >format is just an obstacle and a subjective way of selecting research not >by its quality, but by a "commercial" criterion. > > >Best regards, > > Marc Baaden > > >-- > Dr. Marc Baaden - Labo MSM (UMR 7551) - http://crypt.u-strasbg.fr/marc > mailto:baaden@chimie.u-strasbg.fr - FAX (+49) 40 33 39 68 50 8 > ICQ# 11466242 - Tel: (+33) 6 09 84 32 17 or (+49) 40 33 39 68 50 8 > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > Samuel A. Abrash Associate Professor Department of Chemistry University of Richmond Richmond, VA 23173 Phone: (804) 289-8248 Fax: (804) 287-1897 E-mail: sabrash@richmond.edu http://www.richmond.edu/~sabrash "The time it takes to complete a scientific project is given by the equation t = 2a + b, where a is the original estimate, 2 is a correction factor, and b is a number large compared to 2a." From chemistry-request@server.ccl.net Thu Jan 11 20:44:48 2001 Received: from info.human.nagoya-u.ac.jp (gshi1.info.human.nagoya-u.ac.jp [133.6.48.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0C1igp21223 for ; Thu, 11 Jan 2001 20:44:43 -0500 Received: from 614DELL..info.human.nagoya-u.ac.jp ([133.6.49.29]) by info.human.nagoya-u.ac.jp (8.9.3/3.7W-00060513) with ESMTP id KAA24489 for ; Fri, 12 Jan 2001 10:41:52 +0900 (JST) (envelope-from suresh@info.human.nagoya-u.ac.jp) Message-Id: <4.3.0.20010112104640.00ab88e0@133.6.48.1> X-Sender: suresh@133.6.48.1 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Fri, 12 Jan 2001 10:48:48 +0900 To: chemistry@ccl.net From: sureshch Subject: CCL:document format for ACS journals? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed There is a say 'Even if thousands of convicts are escaped, one innocent should not be punished'. In a similar sense, we can say that 'Even if thousands of worthless papers are accepted by a journal, one worthwhile should not be rejected just because it was not using the correct document format!' ----------------------------------------------------- Suresh C. H. Graduate School of Human Informatics Nagoya University, Chikusa-ku Nagoya 464-8601, Japan Phone: +81-52-789-4810 (off.) 090-4255-4028 (mobile) Fax: +81-52-789-4234 ------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jan 11 21:02:42 2001 Received: from songsim.cuk.ac.kr ([203.229.207.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0C22ep21255 for ; Thu, 11 Jan 2001 21:02:41 -0500 Received: from songsim.cuk.ac.kr ([210.179.239.119]) by songsim.cuk.ac.kr (8.9.3/8.9.3) with ESMTP id LAA09431 for ; Fri, 12 Jan 2001 11:01:53 +0900 (KST) Message-ID: <3A5E65E6.908B8208@songsim.cuk.ac.kr> Date: Fri, 12 Jan 2001 11:03:18 +0900 From: young X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: g98A.9 NBO4.0 problem Content-Type: text/plain; charset=EUC-KR Content-Transfer-Encoding: 7bit Dear everyone I compiled NBO4.M in g98A.9 on dec alpha 4.0D I want to see natural steric analysis I compiled successfully. but it can't calculate natural steric analysis. It can calculate NBSTER but it can't calculate WORTUN especially Ow(-1) matrix. "Cannot form Ow(-1) matrix; aborting SR WORTUN" message is out what is problem? -this is my input file- # hf/3-21G* pop=nboread hydrazine NMR efg calculation from h0irc631d.out 0 1 N N,1,R2 H,1,R3,2,A3 H,2,R4,1,A4,3,D4,0 H,1,R5,2,A5,4,D5,0 H,2,R6,1,A6,5,D6,0 Variables: R2=1.483160 R3=1.020650 R4=1.020650 R5=1.020650 R6=1.020650 A3=104.334840 A4=104.334840 A5=104.334840 A6=104.334840 D4=-71.784510 D5=180.000000 D6=71.784510 $NBO STERIC $END -- ***************************************** Jee-Young Lee The Catholic University of Korea Department of Chemistry Ph.D candidate Tel. +82-32-3403-674 *****************************************