From chemistry-request@server.ccl.net Thu Feb 10 23:56:18 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA26444 for ; Thu, 10 Feb 2000 23:56:17 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id TAA17285; Thu, 10 Feb 2000 19:48:36 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14499.34451.820532.198159@lrz.uni-muenchen.de> Date: Thu, 10 Feb 2000 19:48:35 -0800 (PST) To: Suzanne Sirois Cc: chemistry@ccl.net Subject: CCL:RE:Anybody agrees with me In-Reply-To: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> References: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid [From coordinator: This message got stuck for 2 days, I am very sorry...] Suzanne Sirois writes: > In my opinion there is two life sciences area of applications that > currently need standards: > 1) GUI > 2) Methods > > This sounds to me like classes in OOP. I would like to use this opportunity to alert bioinformatics people about the existance of http://bioperl.org/ and http://biopython.org/ which currently both undergo rapid development, and are likely to become useful in near future, if not already. The only way to push open standards realistically, whether in GUIs or deep code internals, is Open Source. There are a wealth of packages already available (a small selection of what is actually out there) those without the trailing red $$$ at http://sal.kachinatech.com/Z/2/index.shtml though typically the interactivity/GUI concept of free code is somewhat underdeveloped. However, this is nothing intrinsical, nothing which can't be fixed with a bit of effort. Here at CCL, both the developer and user communities are present, sometimes within the same person. I think this is a unique opportunity to get organized. Don't expect the vendors do it for you, because both the concept of OpenSource and the comparatively small user community (no economies of scale) make OpenSource an attractive development option for commercial software developers. Regards, Eugene Leitl From chemistry-request@server.ccl.net Sun Feb 13 02:51:00 2000 Received: from public.online.sh.cn (mail2-px.online.sh.cn [202.96.209.67]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA03535 for ; Sun, 13 Feb 2000 02:50:47 -0500 Received: from cadd ([202.109.46.102]) by public.online.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with SMTP id <0FPU00ERQW71ID@public.online.sh.cn> for CHEMISTRY@www.ccl.net; Sun, 13 Feb 2000 14:47:26 +0800 (CST) Date: Sun, 13 Feb 1994 14:46:38 +0800 From: Haitao Ji Subject: help! Thanks! To: "CHEMISTRY@www.ccl.net" Message-id: <0FPU00ERTW71ID@public.online.sh.cn> Organization: School of pharmacy, second military medical university MIME-version: 1.0 X-Mailer: FoxMail 2.1 [cn] Content-type: text/plain; charset=GB2312 Content-transfer-encoding: 7bit Hi, Now, I want to study the interaction of some ligands with metalloprotein containing metal. However, I donnot know how to get the AMBER force field parameters for metal cobalt. Can you kindly give me suggestion? sincerely, Haitao Ji, Ph.D. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Assistant professor School of pharmacy Second military medical university 325 Guohe Road, Shanghai 200433 P. R. China e-mail: jihaitao@online.sh.cn ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Sun Feb 13 09:30:56 2000 Received: from pae102.ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE [134.130.100.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA06335 for ; Sun, 13 Feb 2000 09:30:55 -0500 Received: from localhost (krzys@localhost) by pae102.ac.rwth-aachen.de (8.9.3/8.9.3) with ESMTP id NAA12544 for ; Sun, 13 Feb 2000 13:20:38 +0100 Date: Sun, 13 Feb 2000 13:20:38 +0100 (CET) From: Tatus To: chemistry@ccl.net Subject: Problem with IRC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers I've got problem with interpretation of my calculation with IRC-path. For one of my compounds I've done vibrational- analysis for one Cs-symmetrical geometry. The negative vibration-mode points on C1-deformation - the one that I would expect. To be sure I've submited it to IRC calculaion. What I see is stange for me. The first point on the path goes in "correct" direction but than the 2nd comes back to starting point. This oscilation are contuinously repeated and I'm still in starting point. All calcualtion was done with Gaussian98.a7 Any sugestions ? Thanks in advance Krzys Radacki _______________------------------------------------------- --------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------- From chemistry-request@server.ccl.net Sun Feb 13 07:32:18 2000 Received: from c008.sfo.cp.net (c008-h013.c008.sfo.cp.net [209.228.14.202]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA05833 for ; Sun, 13 Feb 2000 07:32:18 -0500 Date: Sun, 13 Feb 2000 07:32:18 -0500 From: alb@cristal.org Message-Id: <200002131232.HAA05833@server.ccl.net> Received: (cpmta 23890 invoked from network); 13 Feb 2000 03:27:11 -0800 Received: from r1m103.cybercable.tm.fr (HELO cristal.cybercable.tm.fr) (195.132.1.103) by smtp.cristal.org with SMTP; 13 Feb 2000 03:27:11 -0800 X-Sent: 13 Feb 2000 11:27:11 GMT Identité Message:<4.0.1.20000213110510.00e4ac50@mail.cristal.org> X-Sender: pop@mail.cristal.org(Non vérifié) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Sun, 13 Feb 2000 12:26:40 +0100 To: chemistry@ccl.net From: Armel Le Bail Subject: Re: CCL:RE:Anybody agrees with me References: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Eugene Leitl wrote: >The only way to push open standards realistically, whether in GUIs or >deep code internals, is Open Source. >... >though typically the interactivity/GUI concept of free code is >somewhat underdeveloped. However, this is nothing intrinsical, nothing >which can't be fixed with a bit of effort. A few discordant opinions, I am not at all optimistic about free as opposite to commercial software and GUIs: More than a bit of effort would be needed ! Old academic research ideas of free circulation of software are continuously decreasing, in spite of Linux. And Linux will probably not stay that cheap after its introduction on the Wall Street market... Seems to me that the reason why free circulation is decreasing is exactly because of GUIs. Graphical user interfaces are not at all always necessary in old fashion calculations which just need two files which can be edited by a simple ASCII editor : - datafile - parameters and command file Your just have then to run the program and obtain the result in new files, printable or viewable by some displaying software. Unfortunately, programs are bought by deciders. Deciders have not necessarily any skill in the domain for which they are in charge to buy software. They are very sensitive to shiny GUIs and I suspect they make decision on that aspect of the programs. A lot of chemistry programs are more and more expensive (>1000 US$). Some are even inaccessible. For instance the Cerius2 suite from MSI has satellites attaining almost 50000 US$ for 3 years (PowderSolve). Only ten or so of the biggest pharmaceutical companies could afford it. Free software exist for academic research, doing almost the same, if not better, but without any GUI (running with a command line, in a DOS box and so on). Having to buy programs, you also try to sell your own programs... and this is a vicious circle. Building a museum of more or less old and famous source codes in crystallography shows that most are Fortran codes. http://sdpd.univ-lemans.fr/museum/ Very few GUIs under some Visual Fortran exist, none is open. The scientific global community market has never seemed attractive to Microsoft who abandoned its Fortran compiler. The Digital Visual Fortran compiler inherited of that vacant place, but Digital is also a company a bit losing speed, now in the Compaq basket. A bad new is the recent cancelled publication of a book I was expecting : "Modern Fortran Programming with Digital Visual". The fact that very few of the legacy Fortran code was ported by academic researchers to modern GUI versions is significant of either they consider GUIs not really useful or they consider that programming is the affair of programmers, and programming was not at all or not enough introduced in the learning cursus of chemists. The consequence is today that laboratories and also school budgets are crunched more and more deeply by commercial software and databases expenses. Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France http://www.cristal.org/