From praa2@cluster1.urz.uni-halle.de Tue Mar 21 04:14:12 1995 Received: from mlucom.urz.uni-halle.de for praa2@cluster1.urz.uni-halle.de by www.ccl.net (8.6.10/930601.1506) id DAA05414; Tue, 21 Mar 1995 03:23:51 -0500 From: Received: from cluster1.urz.Uni-Halle.DE by mlucom.urz.uni-halle.de with SMTP (1.36.108.7/15.6) id AA18125; Tue, 21 Mar 1995 09:22:23 +0100 Posted-Date: Tue, 21 Mar 1995 09:24:02 +0100 (MEZ) Received-Date: Tue, 21 Mar 1995 09:22:23 +0100 Received: by cluster1.urz.uni-halle.de (AIX 3.2/UCB 5.64/4.03) id AA21148; Tue, 21 Mar 1995 09:24:03 +0100 Message-Id: <9503210824.AA21148@cluster1.urz.uni-halle.de> Subject: new version of DeFT available To: chemistry@ccl.net Date: Tue, 21 Mar 1995 09:24:02 +0100 (MEZ) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 752 Dear colleagues, since several days I'm using DeFT-code from Alain St-Amant, provided by a colleague of mine, for some test calculations. Unfortunately my colleague do not know exactly , if this is the latest available release. He told me that his version is from Febr./March of the last year. So there is my question. Is this version the actual release or if not where I can get a newer version. I have tried to contact Dr. St Amant directly, but since several weeks I do not get any response. It seems that he is very busy. So I was wondering if there is someone out there to share his/her knowlegde about the various ?? releases of DeFT with me. Any hints or information are highly appreciated. Many thanks for your effort Yours Peter From winnpx@postman.essex.ac.uk Tue Mar 21 07:14:11 1995 Received: from postman.essex.ac.uk for winnpx@postman.essex.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA07039; Tue, 21 Mar 1995 06:19:48 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <15555-0@postman.essex.ac.uk>; Tue, 21 Mar 1995 11:19:16 +0000 From: Winn P J Date: Tue, 21 Mar 95 11:19:10 GMT Message-Id: <6913.9503211119@solb1.essex.ac.uk> To: chemistry Subject: BSSE:summary and thanks. It seems the replies to my BSSE question have dried up, so I think it is now appropriate to thank everyone who responded. A lot of people emailed me to ask for a summary of the replies I got so I enclose this below. Here's one more quick question aswell. How do people expect BSSE to affect various order multipoles??? Significantly or barely at all? Thanks again to everyone who replied. Peter Winn. References and replies. van lenthe et al in vol 2 of Ab Initio Methods in Quantum Chemistry (ed by K. P.Lawley, Wiley press , 1987 (SUMMARY) - "Gaussian Basis sets for Molecular Calculations", S. Huzinaga, Elsevier (1991) - "Ab Initio Calculations", P. Carsky and M. Urban, Springer- Verlag, Lecture Notes in Chemistry, 1980. - "Intermolecular Complexes", P. Hobza and R. Zahradnik, Academia, Prague (1988) Chemical Reviews Nov. 1994 entitled "(v/V!)an der Waals Molecules II Chem Phys Lett 217, 48 (1994) S. Chakravorty, Davidson. Also a reply by Gutowski J Phys Chem 1993 97 11415 J Phys Chem 1993 97 7499 Chem Phys Letters 1990 172 487 J Chem Phys 1987 87 3569 Int J Quant Chem, Quant Chem Symposium 1992 26 527 J Phys Chem 1993 97 107 Chem Phys Lett 1991 183 449 Chem Rev 1988 88 871 Theochem 1994 113 107 J Chem Phys 1993 98 2170 J. E. Del Bene, Int. J. Quantum Chem. Quantum Chem. Symp. 26, 527 (1992). J. E. Del Bene, J. Phys. Chem. 97, 107 (1993). J. E. Del Bene and I. Shavitt, J. Mol. Struc. (Theochem) 307, 27 (1994). State of the Art in Counterpoirse Theory F. B. van Duijneveldt, J. G. M. van Duijneveldt-van de Rijdt and Joop van Lenthe (what a nice collection os "van's"!) Chem. Rev., 94 (1994) 1873-1885 scheiner@qm.c-chem.siu.edu In general, one can expect intermolecular distances to be slightly too short, and interaction energies to be inflated if bsse is not removed. the magnitude of this error is variable; it can be as much as several kcal/mol. while very very large basis would tend to minimize the error, it does not go down smoothly unfortunately. that is, addition of polarization or diffuse functions can increase, rather than decrease, the error. it is common for people to optimize the geometry without correcting the error, but then do a counterpoise calculation at this optimized geometry. this seems to work pretty well most of the time. also be aware that bsse tends to be considerably larger at correlated than at hartree-fock levels. From mrigank@imtech.ernet.in Tue Mar 21 15:14:43 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id OAA16676; Tue, 21 Mar 1995 14:49:27 -0500 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id BAA01738 for chemistry@ccl.net; Wed, 22 Mar 1995 01:19:16 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA13078; Tue, 21 Mar 95 23:30:50+050 Message-Id: <9503211830.AA13078@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 21 Mar 95 09:23:48 +0530 Date: Tue, 21 Mar 95 09:23:48 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:H-bond analysis of MD X-Vms-Mail-To: UUCP%"bishop@london.ks.uiuc.edu" ==>dear netters, ==> ==>I am looking for a program which takes an x-plor format ==> ==>molecular dynamics trajectory file (a DCD file), determines ==>the hydrogen bonds and formats the output in a suitable fashion ==>for reporting. ==>(This information can be extracted from x-plor but it's no simple matter ==>to accumulate the data in a reportable format, as far as I know) ==> ==>The system we wish to analyze contains DNA and excess water and we would like ==>to analyze only the h-bonding of the water to the DNA, and not DNA-DNA h-bonds ==>or water-water hbonds. ==> ==>Any suggestions would be very much appreciated. In my previous organization, I have written a package in Fortran 77 called DNAlys which include this, it was mainly to read AMBER/GROMOS files but X-Plor can be introduced without difficulty. Only due ti some mishap I lost the tape, you can contact DR. V. Kothekar at koth@medinst.ernet.in or vkoth@aiims.ernet.in and seek the program if desired, she might be having a copy. Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From GAO_YING-DUO_NONLILLY@Lilly.com Tue Mar 21 15:14:46 1995 Received: from Lilly.com for GAO_YING-DUO_NONLILLY@Lilly.com by www.ccl.net (8.6.10/930601.1506) id PAA17008; Tue, 21 Mar 1995 15:11:19 -0500 From: Received: from DECNET-MAIL (RXX2505@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HOEHJZ740G000095@INET.D48.LILLY.COM>; Tue, 21 Mar 1995 15:10:46 -0500 (EST) Date: Tue, 21 Mar 1995 15:10:46 -0500 (EST) Subject: Summary of modeling on A-beta Amyloid To: chemistry@ccl.net Message-id: <01HOEHJZ7NAQ000095@INET.D48.LILLY.COM> X-VMS-To: IN::"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Two weeks ago, I submitted a question about modeling on A beta Amyloid. I only got three responses, and two of them are asking a summary of the respose. Anyways, many thanks to everyone who responsed me, especially to Roger Mee. Yingduo Gao ydg@lilly.com 317-277-3439 (o) 317-277-1125 (FAX) ************** 1 **************** >From "D.Winkler@chem.csiro.au" Please do, or at least send me a copy of the responses. Thank you. ************** 2 **************** >From "roger@proteus.co.uk" "Roger Mee" Hi, I have had a little interest in this area. I did some work in which I carried out MD simulations on the Tm domain of beta amyloid and a number of then known familial mutants. The idea was to identify differences in conformational propensity between mutants and normal beta amyloid and so perhasp get some sort of an idea on the effect at a structural level of these mutations. There seemed to be some trends there towards mutants inducing a greater destabilisation of a helix, the degree of which may have correlated with age of onset data fro the various forms. I wrote up this for a poster at the 1992 US Neuroscience meeting put didn't follow it up as it wasn't deemed particularly commercially relevant to us at Proteus. Also the following was posted some time ago.. From: BILL WELSH Dear Netters, I would appreciate hearing about any recent (1990+) published work on Alzheimer's and related diseases that employs computational chemistry, molecular modeling, and/or computer-aided drug design methods. Thanks. Bill Welsh Dept. of Chemistry Univ. of Missouri-St. Louis St. Louis, MO 63121 (314) 553-5318 Bill may be worth contacting to see if he has progressed with this. I'll be interested to know if there has been interesting modelling work done on this. Roger ************** 3**************** >From "mrigank@imtech.ernet.in" "Mrigank" Pls. send me the summary. I am interested in same Mrigank From: GAO YING-DUO NONLILLY (MCVAX0::RXX2505) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") From HASAN@SBMM1.UCSB.EDU Tue Mar 21 16:14:19 1995 Received: from SBMM1.UCSB.EDU for HASAN@SBMM1.UCSB.EDU by www.ccl.net (8.6.10/930601.1506) id PAA17595; Tue, 21 Mar 1995 15:33:30 -0500 Date: Tue, 21 Mar 1995 12:28:20 -0800 (PST) From: MUHAMMAD To: chemistry@ccl.net Message-Id: <950321122820.2020552f@SBMM1.UCSB.EDU> Subject: Geometry optimization Dear netters I'm trying to optimize a geometry with high level of theory such as MRSDCI and the program i'm using can't do analytical or even numerical gradient's so i have to do that by hand ( more than 4 variables) . The question is there any program out there to do this type of optimization such as finite difference methods or any other methods. thanks, Muhammad hasan UCSB Chemistry Dept. e-mail: hasan@sbmm1.ucsb.edu From lerner@emerald.gene.com Tue Mar 21 16:18:35 1995 Received: from genie.gene.COM for lerner@emerald.gene.com by www.ccl.net (8.6.10/930601.1506) id PAA17824; Tue, 21 Mar 1995 15:48:40 -0500 Received: from emerald.gene.com by genie.gene.COM (8.6.9/GSC4.0) id MAA20985; Tue, 21 Mar 1995 12:48:39 -0800 Received: from [128.137.52.49] by emerald.gene.com (8.6.9/GSC4.0) id MAA16032; Tue, 21 Mar 1995 12:48:37 -0800 Message-Id: <199503212048.MAA16032@emerald.gene.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 21 Mar 1995 12:45:03 -0800 To: molecular-dynamics-news@mailbase.ac.uk, chemistry@ccl.net From: lerner@emerald.gene.com (laura lerner) Subject: Meeting Announcement: Physical Chemistry of Proteins, April 2-3, Anaheim ACS Dear Reader, I would like to call your attention to a symposium on the Physical Chemistry of Proteins which will be held Sunday-Monday April 2-3, 1995, at the ACS National Meeting in Anaheim. The complete schedule was published in the March 6 edition of C & E News. The symposium will focus on interdisciplinary applications of physical chemistry to the study of proteins: protein structure, function, dynamics, and interactions. The purpose of this symposium is to foster discussion between biophysical chemists who work on proteins and those physical chemists who do not, but who are interested in moving into biological areas. As the organizer, I have asked the speakers to provide the audience with a sense of where the frontiers in protein science are, and where physical chemistry can push those frontiers further. This symposium is also unusual in its emphasis on new investigators. The goal of the Symposium on the Physical Chemistry of Proteins is to generate informal, fruitful discussions among researchers of diverse backgrounds. Your participation would be welcome! Sincerely, Laura Lerner Genentech, Inc. 415 225-3052 415 225 3554 (fax) lerner@emerald.gene.com Genentech, Inc. Mail Stop 62 460 Point San Bruno Boulevard South San Francisco CA 94080 415-225-3052 From cmartin@rainbow.uchicago.edu Tue Mar 21 17:14:20 1995 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.10/930601.1506) id QAA19770; Tue, 21 Mar 1995 16:56:59 -0500 Received: from rainbow.uchicago.edu (rainbow.uchicago.edu [128.135.136.33]) by midway.uchicago.edu (8.6.10/8.6.4) with SMTP id PAA27786; Tue, 21 Mar 1995 15:56:59 -0600 Received: by rainbow.uchicago.edu (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA11052; Tue, 21 Mar 95 15:56:15 -0600 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9503212156.AA11052@rainbow.uchicago.edu> Subject: Re: CCL:Geometry optimization To: HASAN@SBMM1.UCSB.EDU (MUHAMMAD) Date: Tue, 21 Mar 1995 15:56:15 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <950321122820.2020552f@SBMM1.UCSB.EDU> from "MUHAMMAD" at Mar 21, 95 12:28:20 pm X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 725 > Muhammad hasan writes: > > I'm trying to optimize a geometry with high level of theory such as MRSDCI > and the program i'm using can't do analytical or even numerical > gradient's so i have to do that by hand ( more than 4 variables) . > The question is there any program out there to do this type of optimization > such as finite difference methods or any other methods. > > thanks, > > The latest version of COLUMBUS can do analytical MRSDCI grdients. You will need to contact Hans Lishka at the University of Vienna or Ron Sheppard at Argonne (shepard@tcg.anl.gov) to obtain this version. Regards Chuck Martin Theoretical Biophysics The Beckman Institute The University of Illionis at Urbana-Champiagn From THPierce@RohmHaas.Com Tue Mar 21 17:20:29 1995 Received: from atlas.br.RohmHaas.Com for THPierce@RohmHaas.Com by www.ccl.net (8.6.10/930601.1506) id QAA18678; Tue, 21 Mar 1995 16:18:56 -0500 Received: from rcsh01.sh.rohmhaas.com by atlas.br.RohmHaas.Com (AIX 3.2/UCB 5.64/4.03) id AA21366; Tue, 21 Mar 1995 16:12:20 -0500 Date: Tue, 21 Mar 1995 16:12:20 -0500 Message-Id: <9503212112.AA21366@atlas.br.RohmHaas.Com> X-Sender: rs0thp@monte.br.rohmhaas.com (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu From: THPierce@RohmHaas.Com (Tom Pierce) Subject: Call for Abstracts - Chemistry on the InfoBahn X-Mailer: Call for Abstracts: The Computers and Chemistry Division of the ACS is sponsoring a "Chemistry on the InfoBahn" symposia at the August '95 ACS Meeting in Chicago. We are planning for one day of oral presentations and and electronic presentation session for multimedia articles and posters. The focus of the symposium is on using the Internet to teach/publish/and probe chemical topics and issues. The ACS meeting will be connected to the Internet during the conference, If possible we will broadcast (MBONE) a few of the talks "live" over the Internet. To participate, send in an abstract Real Soon Now (by April 19th). Examples of electronic presentations are at: http://www.ch.ic.ac.uk/talks/ Send an ACS Paper Abstract to a session chair, either: Dr. Thomas Pierce Rohm and Haas Co. P.O. Box 219 Bristol, PA 19007 U.S.A Prof. Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 U.S.A Prof. Henry Rzepa, Dept. of Chemistry Imperial College, LONDON SW7 2AY Great Britain I (thpierce@rohmhaas.com) am working on an electronic submission form, but if you have a paper form that would be safer. Reprise Chemistry on the InfoBahn at the ACS Chicago Meeting, August 20-24 1995 |*| A 150-word abstract on ACS Abstract |*| Form are due by April 19, 1995 ** Chemistry on the Infobahn - Dr. Thomas Pierce, Rohm and Haas Co. P.O. Box 219 Bristol, PA 19007; Voice: (215) 785-8989; FAX (215) 781-4204; email: thpierce@rohmhaas.com, Steven Bachrach, Department of Chemistry, Northern Illinois University, DeKalb, Il 60115;voice: (815)753-6863; Fax: (815)753-4802; email: smb@smb.chem.niu.edu, Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; voice: (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804; email: rzepa@ic.ac.uk, World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html. -- Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist "These opinions are those of the writer and not the Rohm and Haas Company." From watpe@stamail1.vut.edu.au Tue Mar 21 18:14:23 1995 Received: from wolf.vut.edu.au for watpe@stamail1.vut.edu.au by www.ccl.net (8.6.10/930601.1506) id RAA20497; Tue, 21 Mar 1995 17:32:07 -0500 Received: from elk.vut.edu.au by wolf.vut.edu.au (AIX 3.2/UCB 5.64/4.03) id AA34157; Wed, 22 Mar 1995 09:29:47 -0600 Received: from stamail1.vut.edu.au ([140.159.65.21]) by elk.vut.edu.au (4.1/SMI-4.1) id AA09809; Wed, 22 Mar 95 08:30:23 EST Received: by stamail1.vut.edu.au with Microsoft Mail id <2F704D2F@stamail1.vut.edu.au>; Wed, 22 Mar 95 08:15:43 PST From: "Watkins, Peter" To: chemistry@ccl.net Subject: CC in Australia Date: Wed, 22 Mar 95 09:39:00 PST Message-Id: <2F704D2F@stamail1.vut.edu.au> Encoding: 13 TEXT X-Mailer: Microsoft Mail V3.0 I am a relative newbie to the list and have been 'lurking' for a short while. I have an interest in the use of computers in chemical applications. However, most of the postings seem to originate from the northern climes. I would be interested to 'hear' from anyone in Oz who has an interest in this area. I will summarise for the list at a later stage. Regards, Peter Watkins e-mail : watpe@stamail1.vut.edu.au watpe@cougar.vut.edu.au From bkarlak@ren.onyx-pharm.com Tue Mar 21 20:14:20 1995 Received: from iserver.onyx-pharm.com for bkarlak@ren.onyx-pharm.com by www.ccl.net (8.6.10/930601.1506) id TAA21862; Tue, 21 Mar 1995 19:47:52 -0500 Received: from ren.onyx-pharm.com by iserver.onyx-pharm.com (8.6.10/1.37) id QAA15820; Tue, 21 Mar 1995 16:47:52 -0800 Received: by ren.onyx-pharm.com (931110.SGI/921111.SGI.AUTO) for @iserver.onyx-pharm.com:chemistry@ccl.net id AA13740; Tue, 21 Mar 95 16:47:21 -0800 From: "Brian Karlak" Message-Id: <9503211647.ZM13738@ren.onyx-pharm.com> Date: Tue, 21 Mar 1995 16:47:20 -0800 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Depository for analytic & NMR data . . . Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Does anyone know of a depository for NMR and other analytic data that can be searched by compound structure or name? Non-commercial sources are preferred, of course, but commerical refernces would also be appreciated. Also, does anyone have contact information for the Cambridge Crystallographic Database? Do they have a Web site? Thank you very much, Brian Karlak Onyx Pharmceuticals -- "Update all information. Pod into cosmos." Jeffffff said it. i believe it. That settles it. From tony@schroeder.newcastle.edu.au Tue Mar 21 20:17:26 1995 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.10/930601.1506) id UAA22227; Tue, 21 Mar 1995 20:06:52 -0500 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA18418; Wed, 22 Mar 1995 11:06:38 +1000 Date: Wed, 22 Mar 1995 11:06:38 +1000 (EET) From: Tony Dyson To: Computational Chemistry List Subject: CCL: Re:Geometry optimization In-Reply-To: <950321122820.2020552f@SBMM1.UCSB.EDU> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 21 Mar 1995, MUHAMMAD wrote: > Dear netters > > I'm trying to optimize a geometry with high level of theory such as MRSDCI > and the program i'm using can't do analytical or even numerical > gradient's so i have to do that by hand ( more than 4 variables) . > The question is there any program out there to do this type of optimization > such as finite difference methods or any other methods. > If you have the NAG library, there is a routine called E04JAF (I think!) which will take care of this for you. We have used it in the past for performing geometry optimizations with the CRYSTAL92 package, and also with our own old SLAB-MINDO technique. Tony ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================ From aiba@ir.phys.chem.ethz.ch Sun Mar 19 12:56:04 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id MAA09439; Sun, 19 Mar 1995 12:56:01 -0500 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Sun, 19 Mar 1995 18:55:51 +0100 Date: Sun, 19 Mar 1995 18:55:51 +0200 Message-Id: <95031918555104@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net Subject: SUMMARY - MOLECULAR GRAPHICS X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA Dear Netters, on March 14, 1995, I posted a question about molecular graphics packages. The number of specific responses I have received is just 6. However, one can go ahead with it, it seems. I thank all who responded with advices very very much! It's good that good people are reachable through CCL - so CCL must be supported! Some people (seems very young people) wrote to me strange things and I am not posting them. HOW TO READ SUMMARY: - the string of ambersands '&&&&&&&&&&&&&' serves as a delimiter between two separate messages; therefore search please for this string (one of messages is very long&useful). Sincerely, Ayaz Bakasov. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The original posting is this: > Dear Netters, > >could someone advise me please on >a molecular graphics software which: > >a) is ftp-able or commercial, > for a workstation like IBM/RS or Alpha DEC; >b) is for not too large molecules (atoms < 20-30); >c) draws bonds and can mark them (length); >d) draws bond angles and dihedral angles > and can mark them; >c) draws selected planes for pairs of bonds; >e) puts (desirable) different colours > on atoms and marks atoms (for slides); >e) any other useful features on top > of above-specified ones will be welcome > (e.g. animation). > > >Tried RASMOL and found that it is for >VERY large molecules, while I need >to draw molecules ranging from hydrogen peroxide >to some first aminoacids. Also, RASMOL doesn't >take care of small details I am interested in >(like specification of bond angles and > dihedral angles on the graph, or drawing > planes of pairs of bonds) > >Perhaps, Mathematica or Maple >have already some supplementary >packages ?! > >Thank you. >It will be my pleasure to summarize >on the net the suggestions. > >Ayaz Bakasov. > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The responses follow below in chronological ordering: &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 01:19:29.35 From: SMTP%"DOUGH@mdli.com" Subj: ISIS Draw can draw 3D features on structures To: aiba@ir.phys.chem.ethz.ch It doesnt have any rendering capability, but it is designed for generating queries for 3D pharmacophore searching, so distances, angles, dihedrals, lines, planes, centroids, etc can all be drawn, assigned colors, and output to postscript. It is sold thru MDL and thru ACS software (very low price for academics - I think $49). &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 09:28:20.39 From: SMTP%"davide@stinch0.csmtbo.mi.cnr.it" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) Dear Ayaz Bakasov I use SCHAKAL, but I do not think that can write the bond lenghts and angles on the picture. You may contact the author and ask him more information here are some general information and please let me know if you find something. Davide ******************************************************** ************ thank you for your email. Please find attached to this messge some information on the SCHAKAL 92 program. Sincerely -- Egbert Keller | Mail: kell@sun1.ruf.uni-freiburg.de Kristallographisches Institut | University Hebelstrasse 25 | Phone: +49 761 203 6438 D-79104 Freiburg i.Br / Germany | FAX: +49 761 203 6434 -------------------------------------------------------- ------------------- ****************************** Some information on SCHAKAL 92 ****************************** SCHAKAL 92 is a computer program for the graphic representation of molecular and crystallographic models. The most important features of this program are specified in the following. Model types: simple on-screen rotatable wire model, ball-and-stick model with optionally broken, optionally exaggeratedly tapered sticks, space filling model, intersection trace between space filling model and plane. Automatic generation of bonds and specific drawing parameters for the individual types of atoms. Facility to generate packing diagrams and (hkl) surface models. Display styles: outlines; hatching by parallels, meridians, or grids; shading by randomly or regularly dithered dots; "realistic" multi-colour shading. Optional addition of shadows and highlights according to a positionable light source. Optional perspective projections; optional stereo drawings with stereo shading or labelling. Optionally depth-dependent line thickness, darkness, or pseudo-transparency. Rotations: on-screen rotations of wire-models. Several possibilities to align the model, e.g. alignment of a least-squares plane or a crystallo- graphic lattice vector. Optional rotations (or translations) of parts of the model, e.g., rotation of substituents about single bonds. Labelling: facility to label atom circles automatically with atom "names", chemical element symbols, or coordinates, in a manner suitable for publica- tion or documentation (label positions are optimized for minimal overlap. Facility to modify label positions via a graphics cursor. Information: facility to get information on atoms, bonds, model statistics, steric trouble, current switch and parameter settings, view direction, distances, angles, and dihedral angles. Miscellaneous: facility to add cursor-defined lines and cursor-positioned text (e.g. chemical formulas) to the drawing (see figure captions); facility to transform crystallographic coordinates; facility to generate broken-off bond sticks in the boundary region of a model. Various predefined 3D and 2D shading patterns. Data Input: atom names and coordinates; optional: space group symbol or single symmetry operations; input defining a parallelepipedal or polyhedral section of a crystal structure or a (hkl) "surface model". Program control: simple unformatted command code, which allows to vary all important drawing variables and to select individual (or groups of) atoms/ bonds; facility to pick atoms or bonds via a graphics cursor; various "distri- buted command files" for routine tasks; detailed on-line help functions; printed tutorial manual including 24 figures. Output devices: screen; paper plotter (HP-GL file); HP LaserJet III (or fully compatible), screen image save file (non-standard format, described in the manual [except V16version]); .PCX file (V256 version only). Speed: On a 33 MHz 80486 DOS-PC with extended VGA card (1024 x 768), the following times were required to draw a molecule of 100 atoms and 100 bonds on the whole screen (BS = ball+stick model; SP = space-filling model): BS: outlines: 4 sec; fully shaded model incl. shadows and highlights: 22 sec SP: outlines: 4 sec; fully shaded model incl. shadows and highlights: 64 sec Examples: see J. Appl. Crystallography 22, 19-22 (1989) (note: high quality LaserJetIII drawings are not included there) DOS-PC versions *************** There are several DOS-PC versions of SCHAKAL 92 available (none of them is WINDOWS- or network compatible) having a capacity of 1200 atoms and 1200 bonds: a) SCHAKAL 92/V16 for DOS-PC with standard VGA card b) SCHAKAL 92/V256 for DOS-PC with extended VGA card (VESA) c) SCHAKAL 92/FGA4 for DOS-PC with Spea FGA-4 card d) SCHAKAL 92/XXHR for DOS-PC with Elsa XHR Omega/Gemini card Requirements: (1) MS-DOS 5.0 or later; 80386/80387 or 80486 processor (the faster the better) (2) either: a powerful Cache driver (for example MS SMARTDRV.EXE) or: a RAM-disk of at least 1 MB (2 or - better - 4 are recommended). (3) at least 560 kB (573000 Byte) free space within the 640 kB RAM (memory); at least 3 MB free space on your hard disk (much more, if you want to store various plotter or image files). (4) a suitable graphics card. For the different versions, "suitable" means: a) SCHAKAL 92/V16: a standard or extended VGA card; the card will be used with a resolution of 640 x 480 and 16 concurrently displayable colours. b) SCHAKAL 92/V256: an extended VGA card with corresponding colour graphics monitor. The VGA card must correspond to the VESA standard (or run with a VESA driver). SCHAKAL 92/V256 uses VESA modes with 256 concurrently displayable colours and one of the following resolutions: 640 x 480; 800 x 600; 1024 x 768; 1280 x 1024 . A number of VESA drivers for most extended VGA cards will be distributed on the SCHAKAL diskette, packed in a .ZIP file. You will have to "unzip" them with your own PKUNZIP.EXE program. c) SCHAKAL 92/FGA4: A Spea FGA-4 graphics controller or a fully compatible with a resolution of 1280 x 1024 and 256 concurrently displayable colours. d) SCHAKAL 92/XXHR: An Elsa XXHR 110 or XHR Omega or XHR Gemini controller with a resolution of 1280 x 1024 and 256 concurrently displayable colours from a palette of 16 millions. (5) not essential: a plotter which understands HP-GL language or stand-alone software which is able to translate an HP-GL file for your plotter/printer (e.g. PRINTGL from Ravitz Software [shareware]). (6) not essential: an HP LaserJet III or fully compatible printer. The printer must have at least 2 MB memory. (7) not essential, and for SCHAKAL 92/V256 only: a software which is able to copy a .PCX file onto a (colour) printer (e.g. Corel Photopaint by Corel Corporation or Graphics Workshop for WINDOWS by Alchemy Mindworks Inc. [shareware]). Other versions: *************** These consist of the "general FORTRAN code" plus (optionally) an adaption of this code to a certain system (performed by a user of the program). All versions require compilation with a FORTRAN compiler and (possibly) a C compiler. X-Windows versions are comparatively slow; they are, like all other versions, command driven (not menu driven): e) SCHAKAL 92 general FORTRAN code with graphic interface to be adapted to any graphics system f) SCHAKAL 92/AIX-GL GL-version for IBM-RS/6000; requires 3D Adapter SCHAKAL 92/AIX-XW X-Windows version for IBM-RS/6000 g) SCHAKAL 92/IRIS-4D GL-version for Silicon Graphics IRIS-4D h) SCHAKAL 92/SUN X-Windows version for SUN workstations i) SCHAKAL 92/VAX X-Windows version for VAXstations (limited functionality) Note: The author (E.K.) is not able to give any direct support with respect to machine-specific problems for versions f) to i). Some Examples for Commands: *************************** All of SCHAKAL's switches and all parameter settings are controlled by commands, which may be given in arbitrary order. The effect of any command may be altered or cancelled by a command of the same type later on (e.g. after generation of a drawing). Any command begins with two label words which may be followed by parameters, atom codes, and/or bond codes. Note: label words may in any case be abbreviated to one letter. A few examples follow: Genr Unitcell [g u] (add unit cell edges to drawing) Genr Shading [g s] (switch for shaded drawing) Use Commandfile [u c] (execute commands stored on a file) Help U C [h u c] (give information on the 'U C' command) Rot X -12 [etc.] (rotate -12 deg. about X-axis) Rot Bond 80 C2=C7 (rotate substituent 80 degrees about the bond between C2 and C7) Kill Bonds <3.2 Ba=nn (Ba=I (delete bonds between all Ba atoms and other atoms, if dist. <3.2A, but not between Ba and I ) Change Radii *1.15 S1 P (P'2 (increase radii by 1.15 for S1 and P atoms, but not for P atoms belonging to numerical group 2) Xqt Xqt C1-O12 C1-O12=nn (draw all atoms >from C1 to O12 and all the bonds in which they are parti- cipating) Various routine tasks may be accomplished by means of "distributed command files" which contain procedures consisting of large numbers of such commands. An example input to execute such a command file follows (generates a shaded drawing of ball-and-stick plus space-filling model including shadows, highlights, and labelling of non-Hydrogen atoms (see. fig.1)): U C ca w Extent of supply: ***************** A SCHAKAL 92 supply consists of the following items [items a) to i) are distributed on one or two 3.5" DOS diskette(s)]: a) the executable program (DOS versions only) b) the FORTRAN source code of about 35000 lines (all versions except SCHAKAL 92/V16 and SCHAKAL 92/V256) c) an interactive hierarchical on-line manual in English (about 300 pages, if printed) d) a program to make a printout of this manual e) a space group database f) some data set examples g) a number of "distributed command files" for routine tasks h) installation hints and installation program or makefile for the distributed version i) a number of VESA drivers packed into a .ZIP file (SCHAKAL 92/V256 only) j) a printed tutorial manual in English (76 pages, 24 figures) k) printed installation hints for the general version (all versions except DOS versions) Licencing agreement and licence fees: ************************************* SCHAKAL 92 is exclusive property of the University of Freiburg (represented by Kristallographisches Institut der Universitaet). Legal use of the program requires undersigning a licencing agreement and the following licence fees to be paid [in Deutschmarks] (PRI = public research institute): version student school univers. PRI commercial -------------------------------------------------------- --------------------- SCH 92/V16 200.- A) 300.- B) 600.- B) 800.- B) 1200.- A) -------------------------------------------------------- --------------------- SCH 92/V256 250.- A) 375.- B) 750.- B) 1000.- B) 1500.- A) -------------------------------------------------------- --------------------- All other versions 1200.- C) 1600.- C) 2400.- A) -------------------------------------------------------- --------------------- A) valid for installation on one computer. B) valid for installation on a group of PCs to which one "responsible user" has legal and practical access (i.e., all PCs of a work group. If the program is installed on a large network, each workgroup has to pay the licence fee). C) valid for installation on one computer within one unit, where unit is, for example, a department of inorganic chemistry, a dept. of experimental physics, etc. (maximally 2 "Lehrstuehle" = full professorships); a corre- sponding department within a public research institute. A discount of 75 % is offered for installation on a second, third, etc. computer within the same unit. A discount of 60% is offered for a SCHAKAL 92/V16 or SCHAKAL 92/V256 licence within the same unit. For any registered SCHAKAL 86 / SCHAKAL 88 licence, there is an update discount of 75 % on the corresponding licence fee given in the table above (72% for update from SCHAKAL 88B/V16 to SCHAKAL 92/V256). Additional multi-installation discounts are offered for "All other versions" only (87 % discount for 2nd, 3rd, etc. installation). The rules given above are applied to decide whether an installation is a 1st, 2nd, or 3rd (etc.) one and whether a certain (group of) computer(s) is covered by an existing SCHAKAL 88 licence. There is an additional shipment fee of DM 15.- for non-European countries. A 50% discount is offered on all licence fees for East-European and for developing countries. Printing or other kind of multiplication of SCHAKAL drawings ... ... in scientific journals, congress invitations, letters, internally used documents or educational scripts: is generally permitted (except for a student's licence). ... in a scientific textbook: requires payment of an additional licence fee of usually DM 50.- to 500.-, depending on the number of drawings and the scope and purpose of the book. ... in other printed or non-printed matter (especially advertising material): requires payment of an additional licence fee of DM 200.- to 4000.-, the latter amount corresponding to an unlimited printing licence. For commerical users of SCHAKAL 88, the difference between the licence fee for SCHAKAL 88 and for SCHAKAL 92 is accounted for, here. -------------------------------------------------------- ----------- Davide M. Proserpio Dipartimento di Chimica Strutturale e Stereochimica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch.csmtbo.mi.cnr.it -------------------------------------------------------- ----------- &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 15-MAR-1995 17:19:01.12 From: SMTP%"lipkowitz@chem.iupui.edu" Subj: RE: CCL:QUERY - MOLECULAR GRAPHICS To: "Ayaz Bakasov, Phys. Chem., ETH Zurich" Don Boyd has been publishing an updated appendix in every volume of Reviews in Computational Chemistry, published by VCH Publishers. It contains information about many kinds of programs that you might find useful. Good luck, Kenny &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 16-MAR-1995 19:26:20.03 From: SMTP%"heuer@chemie.uni-hamburg.de" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) Dear Ayaz Bakasov Do you have tried xmol for RS6000 it print angles etc if you want it. Ask archie for the location. Yours sincerely Joerg Heuer Ask archie for the location. Joerg Heuer e-mail: Heuer@chemie.uni-hamburg.de Institut fuer Pharmazie, Universitaet Hamburg, Bundesstraae 45, 20146 Hamburg, Germany. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 16-MAR-1995 20:06:10.80 From: SMTP%"dianat@softshell.com" Subj: Re: CCL:QUERY - MOLECULAR GR To: "Ayaz Bakasov, Phys. Chem., ETH" Dear Mr. Bakasov, I am with SoftShell International, we have a program called ChemWindow for the IBM PC or ChemIntosh for the Mac. This is a chemistry drawing program. I will gladly send you a free demo of the program if you are interested, as well as a catalog of our other products. Please let me know, my address is dianat@softshell.com Thank you. ------------------------------ Date: 3/15/95 6:34 AM To: Diana Tarasiewicz From: Ayaz Bakasov, Phys. Chem., ETH &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Date: 17-MAR-1995 17:33:19.03 From: SMTP%"M.J.C.Crabbe@reading.ac.uk" Subj: Re: CCL:QUERY - MOLECULAR GRAPHICS To: aiba@ir.phys.chem.ethz.ch DeskTop Molecular Modeller sounds to be most appropriate. It runs on any PC, uses Windows, and is available from Oxford University Press for about 250 pounds stirling. It is part of a suite of programs and libraries. Contact Mrs Janet Caldwell, Oxford University Press, Walton Street, Oxford, OX2 6DP (tel: +44 (0)1865 56767 for details. Yours, James Crabbe. &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&