From s9610264@cougar.vut.edu.au Fri Aug 8 04:16:16 1997 Received: from fox.vut.edu.au for s9610264@cougar.vut.edu.au by www.ccl.net (8.8.3/950822.1) id DAA15161; Fri, 8 Aug 1997 03:16:29 -0400 (EDT) Received: from cougar.vut.edu.au by fox.vut.edu.au (AIX 3.2/UCB 5.64/4.03) id AA08594; Fri, 8 Aug 1997 17:15:30 +1000 Received: by cougar.vut.EDU.AU (SMI-8.6/SMI-SVR4) id RAA27205; Fri, 8 Aug 1997 17:17:30 +1000 Date: Fri, 8 Aug 1997 17:17:30 +1000 (EST) From: Adnan Hazar To: CCL Subject: HyperNMR Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am trying to perform an NMR run using HyperNMR 2.0 for windows (Win3.1) on minimised conformation of a straight chain molecule (C17 H37 O3 N7). "Shielding and Coupling" calculations take about 2min, however spectrum calculations cannot be performed bec. I get the following message: "There are too many NMR atoms [37]. You may not be able to complete the spectral calculation." As I have been communicating with the software company the problem is that there are too many NMR atoms for the PC configuration I have. Although, I recently upgraded the memory to 64Mb, still not enough simply bec there are 2^37 (1.37xE+11) spin states which require a lot of memory. I'd appreciate any comments which would help me to tackle this problem either at the software or hardware level. Regards ************************ Adnan Hazar Chemical Sciences Victoria University Australia ************************ From hinsen@lmspc1.ibs.fr Fri Aug 8 10:16:25 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id JAA16258; Fri, 8 Aug 1997 09:27:46 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id PAA11216; Fri, 8 Aug 1997 15:28:57 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id PAA22002; Fri, 8 Aug 1997 15:27:15 +0200 Date: Fri, 8 Aug 1997 15:27:15 +0200 Message-Id: <199708081327.PAA22002@lmspc1.ibs.fr> From: Konrad Hinsen To: PDu@synapticcorp.com CC: chemistry@www.ccl.net In-reply-to: <19970722083948.138bb7cb.in@S2> (PDu@synapticcorp.com) Subject: Re: CCL: CCL:Object-oriented means for computational chemist > I found the discussions on OO programming very useful! However, > there is a point that I would like to bring up. That is, is it > possible to implement an OO design using a non-OO language? The main Yes, but it's more difficult and requires more discipline. People who ignore OO language because of the learning curve will probably not prefer OO implementations in non-OO languages. > functions. However, implementing inheritance is impossible without > an OO language. Inheritance is pobably the most important feature of Whether or not inheritance is the most important OO feature is debatable, but it clearly can be implemented in non-OO languages using various pointer tables (that's in fact what OO language compilers produce at the machine language level). Several OO designs have been implemented in this fashion, but you need a good reason to justify the effort. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From hinsen@lmspc1.ibs.fr Fri Aug 8 10:35:11 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id JAA16294; Fri, 8 Aug 1997 09:42:17 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id PAA11295; Fri, 8 Aug 1997 15:43:27 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id PAA22036; Fri, 8 Aug 1997 15:41:59 +0200 Date: Fri, 8 Aug 1997 15:41:59 +0200 Message-Id: <199708081341.PAA22036@lmspc1.ibs.fr> From: Konrad Hinsen To: shenkin@still3.chem.columbia.edu CC: CHEMISTRY@www.ccl.net In-reply-to: <9707241548.ZM14628@still3.chem.columbia.edu> (shenkin@still3.chem.columbia.edu) Subject: Re: CCL:Object-oriented means for computational chemist > The issue I was trying to raise is that regardless of whether one > wants to write the front end in C, C++ or Fortran, or anything else, > the language definition of C++ *precludes* writing a linkable code > libraries in C++ if one ever wants to access the library routines > from another language. This is really too bad, because, whether It is not true that the language definition precludes such a mixed-language use; in fact, it doesn't say a single word about it. Which means that providing or not providing such a possibility is left to individual implementations. Basically the problem is that conventional linker technology is insufficient for OO languages. C++ compilers have to use tricks like name-mangling to make it work. But single-executable executables containing libraries etc. are a bit outdated anyway; everyone is moving towards dynamic libraries etc. And OO interfaces between individually compiled code pieces ("components") do exist, e.g. in the form of CORBA, and with restrictions Microsoft's COM. This approach even has the added advantage of guaranteed inter-language compatibility, and even compatibility across operating systems. Plus of course distributed computing over networks. Those who want to see mixed-language OO systems at work, right now and for free, should have a look at the ILU package developed at PARC: ftp://ftp.parc.xerox.com/pub/ilu/ilu.html Also note that ILU supports a non-OO language (C) as well as several OO languages. The two worlds are not incompatible. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From hinsen@lmspc1.ibs.fr Fri Aug 8 10:38:40 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id KAA16541; Fri, 8 Aug 1997 10:13:32 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id QAA11588; Fri, 8 Aug 1997 16:14:42 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id QAA22116; Fri, 8 Aug 1997 16:13:15 +0200 Date: Fri, 8 Aug 1997 16:13:15 +0200 Message-Id: <199708081413.QAA22116@lmspc1.ibs.fr> From: Konrad Hinsen To: campagne@incm.u-nancy.fr CC: chemistry@www.ccl.net In-reply-to: <33DDCC0C.41C6@incm.u-nancy.fr> (message from Fabien Campagne on Tue, 29 Jul 1997 11:55:08 +0100) Subject: Re: CCL:Design/OO/standardization > Development of software for Computational Chemistry > by researchers is usualy focused on new methodologies. > That's a matter of specialization: people who develop > and maintain scientific software have less time to use > these software to applied research than people interested > in applications only. These two communities have distinct > needs: >... The needs are distinct, but that doesn't mean that they can't be dealt with in a single implementation. A well-designed modular system would consist of well-tested high-performance modules for established techniques and experimental modules for experimental techniques. > Computer scientific community uses standardization commitees > that consist of experts in one field talking together until they > agree on a standard: ONE way to do something that meet experts > idea of what is important (performances, reusability, extensability..). That is one possibility, but equally many products are essentially designed by a single person. There are good and bad aspects about both approaches. > What about standardizing interfaces for common algorithms ? > It seems to me that a minimization algorithm looks like > another and should be used the same way from the code > I'm writing (whatever the implementation I actually decide > to retain) Almost. Minimization algorithms do essentially the same job, but require different parameters for controlling convergence, step sizes, etc. And there are many more situations in which various algorithms have almost the same interface. An OO solution to this problem is to encapsulate the algorithm in an object that also stores all the parameters. For example, you could create a "steepest descent object" with a certain parameters and a "conjugent gradient object" with another set of parameters, and then apply the two in exactly the same way to a molecular system. > Couldn't we design our software so that algorithms are > parameters for algorithms (at compile time). Maybe an example Once algorithms are encapsulated in objects, this is trivial: the algorithm object is simply passed as an ordinary parameter. For an example, look at the description of minimizer objects in my Molecular Modelling Toolkit; the relevant page of the manual is http://starship.skyport.net/crew/hinsen/mmtk_manual/dynamics.html. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From turnerm@CRHSC.UMontreal.CA Fri Aug 8 11:16:18 1997 Received: from condor.CC.UMontreal.CA for turnerm@CRHSC.UMontreal.CA by www.ccl.net (8.8.3/950822.1) id KAA16702; Fri, 8 Aug 1997 10:27:01 -0400 (EDT) Received: from slinky (slinky.CRHSC.UMontreal.CA [132.204.82.50]) by condor.CC.UMontreal.CA with SMTP id KAA04793 (8.6.11/IDA-1.6 for ); Fri, 8 Aug 1997 10:25:33 -0400 Received: from calvin by slinky (920330.SGI/5.17) id AA29199; Fri, 8 Aug 97 10:43:09 -0700 Sender: turnerm@CRHSC.UMontreal.CA Message-Id: <33EB5637.41C6@crhsc.umontreal.ca> Date: Fri, 08 Aug 1997 10:24:07 -0700 From: Maria Turner X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: proline kink angle Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! I am interested in measuring the kink angle introduced in an alpha-helix by the presence of a proline residue in a homolgy built model of a G-protein coupled receptor. I have a reference for an algorithm by Chou et al (1984) to find the helical axis, but any more refernces and help would be greatly appreciated. Thanks, Maria -- Maria Turner Centre de Recherche, Hopital du Sacre-Coeur email: turnerm@crhsc.umontreal.ca From nauss@beryllium.crs.uc.edu Fri Aug 8 11:42:30 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id KAA16686; Fri, 8 Aug 1997 10:24:12 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.6/8.8.6) id KAA08150; Fri, 8 Aug 1997 10:24:14 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9708081024.ZM8148@beryllium.crs.uc.edu> Date: Fri, 8 Aug 1997 10:24:13 -0400 Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: More SGI Information X-Zm-Priority: Low Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii In the continuing thread of SGI's "eminent demise" (which I plead guilty to starting), I found this WWW page, URL http://reality.sgi.com/ariel/sgi-myths.html. It is interesting reading about myths regarding SGI. -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From jhempel@cgl.ucsf.edu Fri Aug 8 20:16:22 1997 Received: from socrates.ucsf.EDU for jhempel@cgl.ucsf.edu by www.ccl.net (8.8.3/950822.1) id TAA19681; Fri, 8 Aug 1997 19:29:23 -0400 (EDT) Received: from [128.218.149.74] (mdi-5.ucsf.EDU [128.218.149.74]) by socrates.ucsf.EDU (8.8.6/GSC4.26) with ESMTP id QAA03215 for ; Fri, 8 Aug 1997 16:29:22 -0700 (PDT) X-Sender: jhempel@socrates.ucsf.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Aug 1997 16:36:47 -0700 To: chemistry@www.ccl.net From: "Judith C. Hempel" Subject: UCSFmeetingOCT9,1997 "Computational Methods in Combinatorial Chemistry" San Francisco, CA October 9, 1997 Meeting is organized by Professor I.D. Kuntz of the University of California San Francisco. Speakers/panelists include: David Floyd(Bristol-Myers Squibb), Tack Kuntz (UCSF), Atsuo Kuki (Alanex), Simon Kearsley (Merck), Peter Willett (Univ. of Sheffield), Will Welch (Arris), Ray Salemme (3D Pharm.) Yax Sun (Bristol-Myers Squibb), Jeff Blaney (Chiron), Mark Murcko (Vertex), Jon Ellman (UC Berkeley), Diana Roe (Sandia). To obtain additional information or to register contact Melina OGrady : ogrady@cgl.ucsf.edu fax: 415-502-7457 or visit the UCSF-Molecular Design Institute web page at http://mdi.ucsf.edu Judith C. Hempel, Ph.D. Director, Corporate Scholar Program UCSF-Molecular Design Institute 513 Parnassus Ave., S-926 San Francisco, CA 94143-0446 (tel) 415.502.8396 (fax) 415.476.9124 or 415.502.7457 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For more info on the MDI, check out our WEB page: http://mdi.ucsf.edu email: jhempel@cgl.ucsf.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jhempel@cgl.ucsf.edu Fri Aug 8 20:34:54 1997 Received: from socrates.ucsf.EDU for jhempel@cgl.ucsf.edu by www.ccl.net (8.8.3/950822.1) id TAA19685; Fri, 8 Aug 1997 19:31:24 -0400 (EDT) Received: from [128.218.149.74] (mdi-5.ucsf.EDU [128.218.149.74]) by socrates.ucsf.EDU (8.8.6/GSC4.26) with ESMTP id QAA14034 for ; Fri, 8 Aug 1997 16:31:24 -0700 (PDT) X-Sender: jhempel@socrates.ucsf.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Aug 1997 16:38:49 -0700 To: chemistry@www.ccl.net From: "Judith C. Hempel" Subject: UCSF meeting: Feb 6-7,1998 "Molecular Recognition in Drug Design: Docking and Scoring" San Francisco, CA February 6-7 1998 3rd UCSF Meeting in Computation Approaches to Biological Molecules Meeting is organized by Professor Peter Kollman of the University of California San Francisco. Speakers/panelists include: Josh Boger (Vertex), Jeff Blaney (Chiron),Fred Cohen (UCSF), Ken Dill (UCSF), Gennady Verkhivker(Agouron), Ajay Jain (Metaxen), Peter Kollman (UCSF), Tack Kuntz (UCSF), Mill Lambert (Glaxo Wellcome), Pieter Stouten (DuPont Merck), Barry Honig (Columbia Univ.), Andrew Leach (Glaxo UK), Mark Murcko (Vertex), Chris Culberson (Merck), Peter Grootenhuis (NV Organon) Thomas Lengauer (GMD). To obtain additional information, please contact: Kristina Clarke : kristina@cgl.ucsf.edu or fax: 415-502-4690 > Judith C. Hempel, Ph.D. Director, Corporate Scholar Program UCSF-Molecular Design Institute 513 Parnassus Ave., S-926 San Francisco, CA 94143-0446 (tel) 415.502.8396 (fax) 415.476.9124 or 415.502.7457 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For more info on the MDI, check out our WEB page: http://mdi.ucsf.edu email: jhempel@cgl.ucsf.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~