From chemistry-request@server.ccl.net Fri Jul 9 01:14:50 1999 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA14428 for ; Fri, 9 Jul 1999 01:14:43 -0400 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with SMTP id WAA07824 for ; Thu, 8 Jul 1999 22:09:09 -0700 (PDT) Message-Id: <4.1.19990708221241.017c48a0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 08 Jul 1999 22:16:05 -0700 To: CCL From: Laurence Lavelle Subject: G98W in Background under NT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Has anyone successfully run G98W in background under NT4 Workstation ? In other words start job, log off, then log on to check progress or another user can log on. If I get something to work I'll post it to CCL. Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" From chemistry-request@server.ccl.net Fri Jul 9 03:45:56 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA15766 for ; Fri, 9 Jul 1999 03:45:54 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de; Fri, 9 Jul 1999 09:40:17 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) id JAA10387; Fri, 9 Jul 1999 09:40:15 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <3785A75F.CDABECE2@physik.tu-muenchen.de> Date: Fri, 09 Jul 1999 09:40:15 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: christian , chemistry@ccl.net Subject: Re: Pseudopotentials References: <3.0.1.32.19990708083809.0080e420@onzon.univ-st-etienne.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Christian! Try this page: http://indy2.theochem.uni-stuttgart.de:80/pseudopotentiale/clickpse.html Bye Thomas christian wrote: > Hi everyone, > > i am looking for a pseudopotential for the praseodyme (Pr3+) element, if > anyone can give me some help. > > Thanks in advance > > -= 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 Jul 8 15:11:21 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA08228 for ; Thu, 8 Jul 1999 15:11:21 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id PAA06710 for ; Thu, 8 Jul 1999 15:05:51 -0400 (EDT) Received: from beckett.CERCA.UMontreal.CA (beckett.CERCA.UMontreal.CA [132.204.150.42]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id PAA14269 for ; Thu, 8 Jul 1999 15:05:46 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by beckett.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id PAA01129 for chemistry@ccl.net; Thu, 8 Jul 1999 15:05:45 -0400 (EDT) Message-Id: <199907081905.PAA01129@beckett.CERCA.UMontreal.CA> Subject: Re: pattern recognition and databases To: chemistry@ccl.net Date: Thu, 8 Jul 1999 15:05:45 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers, I wish to extend my thanks to those people who replied to my question. In response to my question: "on the application of Neural Networks or Genetic algorithms or any statistical methods for the discovery of patterns in databases." First, lets mention that there is basically three different approaches for 3D database searching and they are a direct consequence of the fact that the principles that govern ligand-receptor interaction recognition still remain unclear. 1)I.D. Kuntz focusses on the protein-structure-driven shape matching aspects 2)Y.C. Martin focusses on the medicinal perspective (i.e. pharmacophore) 3)P. Willet focusses on the algorithm and information retrieval aspects. You will find a comparison of the three techniques at the URL: htpp://www.netsci.org/Science/Cheimform/feature06.html This reference is not concern with the application on NN or GA to database mining but raises the important point that good ideas translate eventually into good queries. Amongst many references, one very comprehensive article on similarity searching using GA can be found at the URL: http://www.ijc.com/articles/1998v1/37/ The authors use a Genetic Algorithm to align molecules in a large 3D database and assess the relationship between their similarity and biological activity. (Nick Jewell) It will be interesting to know if this approach has been apply with DFT-derived MEP and electron density. A very important link containing a list of Evolutionary Algorithms in Computer-Aided Molecular Design can be found at the URL: http://panizzi.shef.ac.uk/cisrg/links/ea_bib.html and is maintained by David E. Clark. In conclusion, it seems nowadays that one of the most important challenging problem in CADD, CAMD is the scoring function and it is a direct consequence of our understanding of the ligand-receptor interaction. If it is beyond our actual perception and understanding will it be possible to develop and apply searching method such as GAs that will guide us in the comprehension analysis and treatment of very complex system (i.e. discovery of patterns in database for the formulation of novel ideas and better queries.) Kind Regards, ************************************************* * Suzanne Sirois Ph.D. * * Computational (bio) chemistry * * * * Office CERCA/Alliance Pharma * * (Centre de Recherche en Calcul Applique) * * * * e-mail: siroiss@cerca.umontreal.ca * ************************************************* From chemistry-request@server.ccl.net Thu Jul 8 17:38:13 1999 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA10241 for ; Thu, 8 Jul 1999 17:38:12 -0400 Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.3/UCB 8.8.8/8.7) with SMTP id QAA14776; Thu, 8 Jul 1999 16:36:19 -0500 Date: Thu, 8 Jul 1999 16:36:18 -0500 (CDT) From: Tapas Kar To: WeiQuan Tian cc: Max Valdez , Sigismondo Boschi , CHEMISTRY@ccl.net Subject: Re: CCL:Erroneous write. write -1 instead of 50250000 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, This error is due to space in disk. Check what is the limit of a file - is it more than 2GB? Normally freq calculations take more space. Tapas On Wed, 7 Jul 1999, WeiQuan Tian wrote: > Date: Wed, 7 Jul 1999 14:40:34 -0400 (EDT) > From: WeiQuan Tian > To: Max Valdez > Cc: Sigismondo Boschi , CHEMISTRY@ccl.net > Subject: CCL:Erroneous write. write -1 instead of 50250000 > > > Hi, > > Maybe it is not only the problem for disk space. I did a calculation > C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I > am sure that this calculation doesn't need more than 2GB disk space. > However the job stopped at l1002 for the frequency calculation. So I guess > it is due to memory, however, I have 128MB memory in PII350 and I included > 120MB for the calculation. I was confused with this error. As in fact I > met the similar problem with UNIX, while I can't remember how I solved > such a problem. > > Wei Quan Tian > Univ. of GUelph > Canada > -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist/Asst. Professor (Adjunct) Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 9 04:12:01 1999 Received: from balcab1-log3.balcab.ch (dns1.balcab.ch [195.65.227.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA16203 for ; Fri, 9 Jul 1999 04:12:00 -0400 Received: from mdpi.org ([10.0.11.126]) by balcab1-log3.balcab.ch (Netscape Messaging Server 3.6) with ESMTP id AAA1C41; Fri, 9 Jul 1999 10:03:07 +0200 Message-ID: <3785AD57.CC8A83EB@mdpi.org> Date: Fri, 09 Jul 1999 10:05:43 +0200 From: Shu-Kun Lin Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.51 [en] (Win98; I) X-Accept-Language: zh,zh-CN,en-US MIME-Version: 1.0 Subject: Annual Review of Chemical Resources on the Internet Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would like to invite you to contribute short papers for presentation at ECSOC-3 (http://www.mdpi.org/ecsoc-3.htm section E) and for publication in a special issue (December 1999) "Annual Review of Chemical Resources on the Internet" of MOLECULES (http://www.mdpi.org/molecules/). Any suggestions are welcomed. Titles and Topics are Links for Chemists Main website: http://www.liv.ac.uk/Chemistry/Links/links.html Author(s): Michael H. Barker Online-only Journals Monitored by Chemical Abstracts Main website: http://www.cas.org/EO/ejourn2.html Author(s): Nancy Simons Web-Based 2D Structure Registration and Search Main website: http://www.mdpi.org/forum.htm#chemicals Author(s): (Shu-Kun Lin) Online Accessible Chemical Databases Main website: http://www.mdpi.org/forum.htm#chemicals Author(s): (Shu-Kun Lin) Other topics: Electronic Conferences on Chemistry Mailing Lists of Chemistry Chemical Software (Several papers) Chemical Java Applets Web-Based Electronic Laboratory Notebook Online Chemistry Books Web-Reprints of Classical Works New Web-Based Books Databases, websites related to chemistry are very dynamic, ever growing or updating. Let us have a snapshot once every year so that some decades late, to say in 2100, our grand children will have a chance to see how things on the then primitive and exciting internet going. Internet is a large stride of a revolution towards information freedom. The "Annual Review of Chemical Resources on the Internet" also serves as records of the overview of the work of chemistry internet pioneers. Submitted papers can be stored locally on your server. If possible, with the permission of the webmaster, download and store the related websites and put them into your local server The style of the papers should be like that of http://www.unibas.ch/mdpi/molecules/papers/30100016/30100016.htm Try to gather all the links to the "References and Notes" section. The first one will be published as a special issue of Molecules (http://mdpi.org/molecules/) in December 1999. If it its volume is very large, we may treat it as an online book. Interested authors are invited to prepare a chapter. One chapter in the final book is regarded as an independent review paper for Molecules. please contact by e-mail with me for further information. Shu-Kun Lin Managing Editor Molecules (ISSN 1420-3049, CODEN: MOLEFW) http://www.mdpi.org/molecules/ From chemistry-request@server.ccl.net Fri Jul 9 11:45:18 1999 Received: from gatekeeper.bnfl.co.uk (gatekeeper.bnfl.co.uk [193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA22114 for ; Fri, 9 Jul 1999 11:45:17 -0400 From: Scott.L.Owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id QAA19659; Fri, 9 Jul 1999 16:37:39 +0100 (BST) Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper via smap (V2.1) id xma019624; Fri, 9 Jul 99 16:37:20 +0100 Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Fri, 09 Jul 1999 16:42:58 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id QAA12695 for ; Fri, 9 Jul 1999 16:38:55 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002567A9.005B679E ; Fri, 9 Jul 1999 16:38:23 +0000 X-Lotus-FromDomain: BNFL To: chemistry@ccl.net Message-Id: <002567A9.005B1A7F.00@BNotesMTA1.sell.bnfl.com> Date: Fri, 9 Jul 1999 16:38:36 +0000 Subject: List of chemistry software on web MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Does anyone know of a site on the web which lists suppliers/originators of computational chemistry software? I was going to compile one for the Royal Society of Chemistry's website and thought that I should check that such a resource does not already exist. The idea is to compile one which is not linked to any particular vendor or academic group. Thanks in anticipation. From chemistry-request@server.ccl.net Fri Jul 9 11:43:48 1999 Received: from mgcct6.nci.nih.gov (mgcct6.nci.nih.gov [137.187.211.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA22095 for ; Fri, 9 Jul 1999 11:43:48 -0400 Received: from helix.nih.gov (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA05414; Fri, 9 Jul 1999 12:59:34 -0400 Sender: brunob@helix.nih.gov Message-ID: <37862A76.9BA681F7@helix.nih.gov> Date: Fri, 09 Jul 1999 12:59:34 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Peter Shenkin , Computer Chemistry List CC: jvoigt@helix.nih.gov Subject: Re: CCL:Problem with Macromodel on IRIX References: Content-Type: multipart/alternative; boundary="------------898A730CFB578D9E103B8704" --------------898A730CFB578D9E103B8704 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Peter Shenkin wrote: > Hi, > > There is a bug in the -mips4 fast math library (libfastm.so) originally > distributed with IRIX 6.4 (and 6.3). This can be fixed by upgrading to > IRIX 6.5, or by installing patch Patch 1774 or 3131 & 3219, or 2752. (Some of > these may superceded; if so, install the later one(s). But > your best bet is to upgrade. > > BTW, this is Q4.4 on our FAQ page, > http://www.schrodinger.com/MacroModel/faq.html > > Hope this helps, > -P. > Thanks a lot for your quick answer. Thanks also to the two other persons who replied. I installed the patches 3131 and 3219 on the IRIX 6.4 machine. Thereafter, the output of the cyclohexane energy calculation was identical to the one obtained on the IRIX 6.5 machines. The FAQ page, as mentioned by Peter, clearly describes this solution. We are currently checking the patch versions on all our SGI workstations. I feel lucky that I used two different SGI workstations for the same calculation, otherwise I wouldn't have noticed this problem. Does anyone know what functions in the math library (libfastm.so) were broken and which other programs may be affected (e.g CHARMM)? Also, I am looking for a piece of C code that tests the validity of the library by performing a simple math operation related to the broken functions. This code would report an error message and stop the program if the result is not correct. One reason that I'm interested in this (instead of simply applying the patches) is that we run a lot of our programs on various central SGI systems for which we don't have root privileges, and on which the patch situation not known to us offhand, so I want a "hard test" to see if things are alright or not. Another reason is that I would like to incorporate such a test into my own programs which are freely available and might be running by other people on unpatched IRIX machines. I believe that this buggy fast math library is a much more serious problem than the "Pentium bug". Bruno -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://www.brunob.org ] --------------898A730CFB578D9E103B8704 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Peter Shenkin wrote:
Hi,

There is a bug in the -mips4 fast math library (libfastm.so) originally
distributed with IRIX 6.4 (and 6.3).  This can be fixed by upgrading to
IRIX 6.5, or by installing patch Patch 1774 or 3131 & 3219, or 2752. (Some of
these may superceded;  if so, install the later one(s).  But
your best bet is to upgrade.

BTW, this is Q4.4 on our FAQ page,
        http://www.schrodinger.com/MacroModel/faq.html

Hope this helps,
-P.
 

Thanks a lot for your quick answer.  Thanks also to the two other persons
who replied. I installed the patches 3131 and 3219 on the IRIX 6.4
machine.  Thereafter, the output of the cyclohexane energy calculation was
identical to the one obtained on the IRIX 6.5 machines.  The FAQ page, as
mentioned by Peter, clearly describes this solution.  We are currently
checking the patch versions on all our SGI workstations.

I feel lucky that I used two different SGI workstations for the same
calculation, otherwise I wouldn't have noticed this problem.
 

Does anyone know what functions in the math library (libfastm.so) were broken
and which other programs may be affected (e.g CHARMM)?

Also, I am looking for a piece of C code that tests the validity of the
library by performing a simple math operation related to the broken
functions.  This code would report an error message and stop the program
if the result is not correct.  One reason that I'm interested in this
(instead of simply applying the patches) is that we run a lot of our
programs on various central SGI systems for which we don't have root
privileges, and on which the patch situation not known to us offhand,
so I want a "hard test" to see if things are alright or not. Another reason is that I would like to  incorporate such a test into my own programs which are freely available and might be running by other people on unpatched IRIX machines.

I believe that this buggy fast math library is a much more serious problem
than the "Pentium bug".

Bruno
 
 
  

-- 
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : brunob@helix.nih.gov      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]
  --------------898A730CFB578D9E103B8704-- From chemistry-request@server.ccl.net Fri Jul 9 14:47:44 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA24036 for ; Fri, 9 Jul 1999 14:47:34 -0400 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id UAA03034 for ; Fri, 9 Jul 1999 20:45:08 +0200 (MET DST) Date: Fri, 9 Jul 1999 20:41:49 +0200 (MET DST) From: Pablo Vitoria Garcia To: chemistry@ccl.net Subject: Yaehmop compilation on Dec Alpha Message-ID: MIME-Version: 1.0 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 OAA24037 Hi all, I recently dowloaded the source code of the program Yaehmop (an extended Huckel program), but I am unable to compile it on a Dec Alpha, because I don«t know which FLAGS and options to choose in the makefiles provided (for HP, LINUX, AIX,... but not DEC). Did anyone succeded in the compilation? If so, would you be so kind to tell me how to do it? Thank you very much Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Address: Dpto. Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 Fax: +34 94 4648500 -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 9 18:24:20 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA26778 for ; Fri, 9 Jul 1999 18:24:19 -0400 Received: from mayer.scripps.edu (mayer.scripps.edu [137.131.252.36]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id PAA05549 for ; Fri, 9 Jul 1999 15:18:33 -0700 (PDT) Received: (from nwhite@localhost) by mayer.scripps.edu (8.9.2/TSRI-3.0) id PAA21136 for chemistry@ccl.net; Fri, 9 Jul 1999 15:18:32 -0700 (PDT) Date: Fri, 9 Jul 1999 15:18:32 -0700 (PDT) From: Neill White Message-Id: <199907092218.PAA21136@mayer.scripps.edu> To: chemistry@ccl.net Subject: CCL: Biomer - MM/MD on the web X-Sun-Charset: US-ASCII From - Fri Jul 9 18:02:20 1999 X-Mozilla-Status: 0001 X-Mozilla-Status2: 00000000 Message-ID: <378263B8.1B0ABC4C@scripps.edu> Date: Tue, 06 Jul 1999 20:14:48 +0000 Hello CCLers - This is an announcement of the availability of a new molecular modeling program - Biomer - that is accessible over the web. It should be useful as an educational tool as well as a means to generate structures quickly and easily. It is written in Java, and version 1.0a has the following features: Model Builders for: nucleic acids (DNA/RNA) polypeptides polysaccharides Interactive molecule editor with fragment libraries Implementation of the AMBER force field Geometry Optimization with steepest descent / conjugate gradient Simulated Annealing with molecular dynamics Reads / Writes PDB files Exports jpeg, gif, and ppm images It is located at http://www.scripps.edu/~nwhite/Biomer/index.html Regards, Neill K. White From chemistry-request@server.ccl.net Fri Jul 9 18:46:07 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27265 for ; Fri, 9 Jul 1999 18:46:07 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id SAA04637 for ; Fri, 9 Jul 1999 18:40:22 -0400 (EDT) Received: from bizet.CERCA.UMontreal.CA (bizet.CERCA.UMontreal.CA [132.204.150.118]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id SAA04478; Fri, 9 Jul 1999 18:40:21 -0400 (EDT) From: Youliang Wang Received: (from wangy@localhost) by bizet.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id SAA08885; Fri, 9 Jul 1999 18:40:20 -0400 (EDT) Message-Id: <199907092240.SAA08885@bizet.CERCA.UMontreal.CA> Subject: Re: CCL:Java molecule viewer To: CHEMISTRY@ccl.net Date: Fri, 9 Jul 1999 18:40:20 -0400 (EDT) Cc: wangy@CERCA.UMontreal.CA (Youliang Wang) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Mark, You may have a look at java molecule viewer we had. Both applet and applications are available. Please go to the web site below for more details. http://www.wag.caltech.edu/home/wangy/JaMoVe.htm Youliang > Hi everyone. > > For various reasons I would like a Java applet for viewing molecules in 3D. > My requirements are reasonably specific, and include the ability to display > and independently rotate numerous molecules in the same window. I've looked > around, and have yet to see anything that will fit my requirements off the > shelf, so am left with the task of writing my own :). I'm not that good at > Java yet, and would prefer to avoid reinventing the wheel. > > So, does anyone know if there is source code available for even a simple > molecule viewer? For portability reasons I would prefer code that works with > Java 1.1 or older: I've found a few molecule viewers (such as the > publically-released viewer from Tripos) but these all seem to require the > JDK 1.2 and Java3D extension. > > All help appreciated :) > > Mark Mackey. > > -= 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 > > > > > ----- End of forwarded message from Youliang Wang ----- From chemistry-request@server.ccl.net Fri Jul 9 21:34:10 1999 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA28549 for ; Fri, 9 Jul 1999 21:34:10 -0400 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay2.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id SAA06936 for ; Fri, 9 Jul 1999 18:28:22 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by elvis.scripps.edu (8.9.2/TSRI-3.0) with ESMTP id SAA38829 for ; Fri, 9 Jul 1999 18:28:22 -0700 (PDT) Sender: yadavm@scripps.edu Message-ID: <3786A1B6.539995D8@scripps.edu> Date: Fri, 09 Jul 1999 18:28:22 -0700 From: Maneesh Yadav X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: A few more CSD/ACD questions.. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We have obtained a list of structures from the CSD (about 50) that we want to check for commercial availability.. does anyone have a better way of doing this that redrawing them all in ACD / Sci finder? From chemistry-request@server.ccl.net Fri Jul 9 21:38:06 1999 Received: from LMSMRM ([202.127.25.133]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA28613 for ; Fri, 9 Jul 1999 21:38:01 -0400 Received: from LMSMRM (localhost [127.0.0.1]) by LMSMRM (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA03363 for ; Sat, 10 Jul 1999 09:28:16 +0900 Sender: user@iris.sipp.ac.cn Message-ID: <378693A0.41C6@iris.sipp.ac.cn> Date: Sat, 10 Jul 1999 09:28:16 +0900 From: maoxiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: JAVA and OPENGL Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit HI: Here are two questions I need your help. First, where I can download the JAVA for SGI freely. And second, I need to compile some programs need the head file of OPENGL, so where I can find them free of charge. Thanks in advance. Regards, Mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | 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 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~