From jkshin@radon.sait.samsung.co.kr Wed Jan 12 02:49:23 1994 Received: from han.hana.nm.kr for jkshin@radon.sait.samsung.co.kr by www.ccl.net (8.6.4/930601.1506) id BAA04273; Wed, 12 Jan 1994 01:56:53 -0500 Received: from (saitgw.sait.samsung.co.kr) by han.hana.nm.kr (4.1/KUM-0.1) id AA11877; Wed, 12 Jan 94 15:57:59 KST Received: from radon.sait.samsung.co.kr by (4.1/SMI-4.1) id AA16839; Sat, 8 Jan 94 21:43:13 KST Received: by radon.sait.samsung.co.kr (920330.SGI/920502.SGI.AUTO) for @saitgw.sait.samsung.co.kr:chemistry@ccl.net id AA00456; Thu, 13 Jan 94 14:46:06 +0900 Date: Thu, 13 Jan 94 14:46:06 +0900 From: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) Message-Id: <9401130546.AA00456@radon.sait.samsung.co.kr> To: chemistry@ccl.net Subject: Molecular Simulations Dear Netters: Does anybody know about the journal "Molecular Simulations"? Which sorts of papers are reported in that journal and how many issues are published a year? Who is the editor in chief and What is the mailing address to send manuscript? Any sorts of information will be appreciated. Thanks in advance Jai K. Shin jkshin@radon.sait.samsung.co.kr From ernst@bkfug.kfunigraz.ac.at Wed Jan 12 06:49:23 1994 Received: from bkfug.kfunigraz.ac.at for ernst@bkfug.kfunigraz.ac.at by www.ccl.net (8.6.4/930601.1506) id GAA05154; Wed, 12 Jan 1994 06:01:38 -0500 From: Received: by bkfug.kfunigraz.ac.at (MX V3.3 AXP) id 22687; Wed, 12 Jan 1994 12:01:49 --0100 Date: Wed, 12 Jan 1994 12:01:45 --0100 To: Chemistry@ccl.net Message-ID: <009786CB.43C8D868.22687@bkfug.kfunigraz.ac.at> Subject: R2Si=XRn systems Hi, I am presently trying to get an overview of the literature concerned with the class of systems containing a formal double bond Si=X, where X are 2nd and 3rd row main group elements. Of particular interest are calculations concerned with relative stabilities. I am aware of the paper by Schleyer and Kost, J. Am. Chem. Soc. 1988, 110, p2105 and older literature. Not having access to online-CAS makes literature surveys a bit slow, thus this request. Please respond to me directly, and, if you are interested in a summary, send a note as well - I'll summmarize to the net, given enough interest. thanks in advance Margot From wgalazka@chem.uw.edu.pl Wed Jan 12 07:49:23 1994 Received: from sunic.sunet.se for wgalazka@chem.uw.edu.pl by www.ccl.net (8.6.4/930601.1506) id HAA05726; Wed, 12 Jan 1994 07:20:43 -0500 Received: from chem.uw.edu.pl by sunic.sunet.se (8.6.4/2.03) id NAA12368; Wed, 12 Jan 1994 13:20:28 +0100 Received: from [148.81.21.70] (caesar.chem.uw.edu.pl) by chem.uw.edu.pl (4.1/SMI-4.1) id AA18752; Wed, 12 Jan 94 13:12:41 +0100 Organization: Department of Chemistry, University of Warsaw Address: Pasteura 1, 02-093 Warsaw, Poland. From: "Wojciech Galazka" Date: Wed, 12 Jan 94 13:11:41 CST Message-Id: <396.wgalazka@zoolook.chem.uw.edu.pl_POPMail/PC_3.2.3_Beta_2> X-Popmail-Charset: IBM 8-Bit To: Chemistry@ccl.net Subject: Re: Advice - drawing structures under X? On Mon, 10 Jan 94 18:19:33 EST, Raul Valdes-Perez wrote: >As part of a long-term project (MECHEM), we now have a strong need for >some X Windows software that will draw molecular structures [..] >I have searched the archives of this list, but didn't find what we >need. I would appreciate any advice. Thank you. Dear Dr. Raul Valdes-Perez, I suggest you sending your letter to the Xpert disscussion group, its topic of interest is just X-Window Programming. The address is XPERT@EXPO.LCS.MIT.EDU Hope this helps a bit. Wojciech Galazka ///////////////////////////////////////////////////****************** // Wojciech Galazka // * // Computer Center // Chemistry - yes,* // Chemistry Department, University of Warsaw // Distortions- no * // Pasteura 1, 02-093 Warsaw, Poland // * ///////////////////////////////////////////////////****************** From stoutepf@chemsci1.es.dupont.com Wed Jan 12 09:49:24 1994 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.4/930601.1506) id IAA06794; Wed, 12 Jan 1994 08:56:10 -0500 Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991); id AA03962; Wed, 12 Jan 94 08:55:45 -0500 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com (4.1/SMI-4.1) id AA26231; Wed, 12 Jan 94 08:54:02 EST Message-Id: <9401121354.AA26231@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Wed, 12 Jan 1994 08:54:43 -0500 To: chemistry@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: Molecular Simulations Cc: jkshin@radon.sait.samsung.co.kr (Jaikwang Shin) On Thu, 13 Jan 94, Jaikwang Shin wrote: >Does anybody know about the journal "Molecular Simulations"? > I think it is a very good journal. For some unintelligible reason it is far less popular in USA than Europe. >Which sorts of papers are reported in that journal and how many >issues are published a year? > Both theoretical/methods and applications papers, mainly dealing with MD, MM and MC simulations/calculations, force field development, but has also more general modelling papers. The accent is on papers that have both methods and applications in them. Most papers address issues in chemistry, many of them in the area of biomolecules. A very good issue is Volume 10, Number 2-6 (1993), which is a special issue on "Molecular Simulation of Biological Molecules." You should be able to get that issue as a sample copy. Some contributors: van Gunsteren, Nakamura, Kollman, Bruccoleri, Mezei, Stouch and McCammon. >Who is the editor in chief and >What is the mailing address to send manuscript? > Editor in Chief is N. Quirke. manuscripts can be sent to him or to one of the appropriate regional editors (Gubbins, Cornell or van Gunsteren, ETH). I suppose you should submit to Quirke. His address is: BP Research Centre, Chertsey Road, Sunbury-on-Thames, MiddlesexTW16 7LN, England, UK. Hope this helps. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- ARA/Fax: +1 (302) 695 4324 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From davide@stinch0.csmtbo.mi.cnr.it Wed Jan 12 09:52:52 1994 Received: from stinch0.csmtbo.mi.cnr.it for davide@stinch0.csmtbo.mi.cnr.it by www.ccl.net (8.6.4/930601.1506) id JAA07046; Wed, 12 Jan 1994 09:35:14 -0500 From: Received: by stinch0.csmtbo.mi.cnr.it (911016.SGI/911001.SGI) for chemistry@ccl.net id AA04017; Wed, 12 Jan 94 15:11:55 GMT Date: Wed, 12 Jan 94 15:11:55 GMT Message-Id: <9401121511.AA04017@stinch0.csmtbo.mi.cnr.it> To: chemistry@ccl.net Subject: automatic solution of crystal structures : SIR92 & SIRPOW92 Hi, To all the crystallographers and others, I am a very satisfied user of two programs (SIR92 and SIRPOW92)for automatic solution of crystal structures by direct methods, with a very nice graphic interface. The program for single crystal data produces (often with all the atoms assigned and R<10%) input for two commonly used programs for structure refinement SHELX or CRYSTALS For more information see below. Davide Proserpio To obtain a copy please contact Dr Cascarano providing your ftp address. Dr. Gianluca Cascarano Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche CNR, c/o Dipartimento Geomineralogico, Campus Universitario, 70124 Bari, Italy phone +39-80-242624, FAX +39-80-242591 e-mail cryst@arba.ba.cnr.it ***************************************************************** SIR92 - A PROGRAM FOR AUTOMATIC SOLUTION OF CRYSTAL STRUCTURES BY DIRECT METHODS. A. ALTOMARE, G. CASCARANO, C. GIACOVAZZO, A. GUAGLIARDI Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche CNR, c/o Dipartimento Geomineralogico, Campus Universitario, 70124 Bari, Italy, M.C. BURLA, G. POLIDORI Dipartimento di Scienze della Terra, Universita', 06100 Perugia, Italy, M. CAMALLI Ist. di Strutturistica Chimica "G. Giacomello", CNR, Via Salaria Km 29,200, 00016 Monterotondo stazione (Roma), Italy. THE CRYSTALLOGRAPHIC PROBLEM: Our recent developments in direct methods theory and in crystal structure refinement persuaded us to develop a fully automated structure-determination program which is able to solve the phase problem and to refine atomic parameters in a single computer run. METHOD OF SOLUTION: The method for the automatic structure determination is based on the representation theory (Giacovazzo, 1977, 1980). 1-phase structure seminvariants and 3-phase structure invariants are estimated via their second representation, 2-phase seminvariants and 4-phase invariants via their first representation. SIR92 is the heir of SIR88 (Burla, Camalli, Cascarano, Giacovazzo, Polidori, Spagna & Viterbo, 1989) of which it retains most of the features (f.e., treatment of pseudotranslational symmetry, use of prior information, tangent weighting schemes, etc.). In SIR88 1-,2-phase seminvariants and positive estimated 3-phase invariants could be actively used in the phasing process. Negative estimated triplet and quartet invariants were used as a FOM together with psi-zero triplets. In SIR92 negative estimated triplet and quartet invariants and psi-zero triplets are actively used in the phasing process, which proved to be much more robust and efficient. The various trial solutions can be obtained either by magic integer permutation (Main, 1978) or by random phases (Baggio, Woolfson, Declercq & Germain, 1978). The best trial solution, selected by powerful FOM's, is automatically processed through a cyclic procedure combining structure factor calculation - least squares - 2Fo-Fc Fourier synthesis. The final outcome is a set of refined atomic parameters (x,y,z and isotropic B values) associated with suitable atomic species. The residual R value is calculated for user usefulness (final values usually between 0.08 and 0.15). The program runs in default when supplied with a minimum amount of information (space group symbol, cell parameters, unit cell chemical content and reflections) but documentation has been produced to allow the user to change default values. If a graphic device is available the user can follow structure solution and refinement on the screen. In the final stage a menu-driven interface is available in order to study molecular geometry and restart refinement. SOFTWARE ENVIRONMENT: The program has been written in standard Fortran77. A module written in C language is supplied in order to interface the program with X-window or DEC-Window terminals for graphics. Therefore, besides the C compiler, an Xlib library is also needed. Two ASCII files are associated to the program: the first contains coefficients for calculating scattering factors, the second, necessary for graphics, contains on-line help. HARDWARE ENVIRONMENT: The program runs on UNIX and DEC workstations, on mainframe and on personal computers (for this last one 4 Mbytes of RAM and a VGA monitor are needed). PROGRAM SPECIFICATION: The source code of the program consists of 41.000 FORTRAN lines and of 2000 C lines (including comments). DOCUMENTATION: Users instructions and program description (about 1500 lines) are supplied as an ASCII text file. AVAILABILITY: The program is available free of charge from the teams in Bari and in Perugia. A licence agreement has to be signed. REFERENCES Burla, M.C., Camalli, M., Cascarano, G., Giacovazzo, C., Polidori, G., Spagna, R. & Viterbo, D. (1989). J. Appl. Cryst. 22,389-393. Baggio, R., Woolfson, M.M., Declercq, J.P. & Germain, G. (1978). Acta Cryst. A34,883-892. Giacovazzo, C. (1977). Acta Cryst. A33,933-944. Giacovazzo, C. (1980). Acta Cryst. A36,362-372. Main, P. (1978). Acta Cryst. A34,31-38. ***************************************************************** SIRPOW.92 - A PROGRAM FOR AUTOMATIC SOLUTION OF CRYSTAL STRUCTURES BY DIRECT METHODS OPTIMIZED FOR POWDER DATA. A. ALTOMARE, G. CASCARANO, C. GIACOVAZZO, A. GUAGLIARDI Istituto di Ricerca per lo Sviluppo di Metodologie Cristallografiche CNR, c/o Dipartimento Geomineralogico, Campus Universitario, 70124 Bari, Italy, M.C. BURLA, G. POLIDORI Dipartimento di Scienze della Terra, Universita', 06100 Perugia, Italy, M. CAMALLI Ist. di Strutturistica Chimica "G. Giacomello", CNR, Via Salaria Km 29,200, 00016 Monterotondo stazione (Roma), Italy. THE CRYSTALLOGRAPHIC PROBLEM: Solving crystal structures from powder data is not a routinary job: peak overlapping, preferred orientation and difficulties in background estimation make uncertain the evaluation of the diffraction intensities for the various reflections. Consequently both Patterson and direct methods lose efficiency and structure solution is not straightforward. The first aim of this program is to optimize direct methods for powder data. METHOD OF SOLUTION: The standard input of SIRPOW.92 consists of lattice constants, space group, chemical content of the unit cell, and a file of reflections as provided by current peak decomposition programs. Neutron data as well as X-ray data can be managed. The overlapping conditions, chosen by the program or fixed by the user, are stored for subsequent use. For example, /E/'s of some "important" overlapping reflections can be suitably varied in order to generate different phasing pathways. As in SIR92 (Altomare, Cascarano, Giacovazzo, Guagliardi, Burla, Polidori & Camalli, 1994) 1-phase and 2-phase structure seminvariants and 3- and 4-phase structure invariants are estimated via proper representations (Giacovazzo, 1977, 1980). Trial solutions are obtained by the magic integer approach (Main, 1978) or by random phases (Baggio, Woolfson, Declercq & Germain, 1978). The best solution, selected by proper FOM's, is automatically processed through a cyclic procedure integrating structure factor calculation - least squares - 2Fo-Fc Fourier synthesis. Due to reflection overlap the observations in the least squares routine are the total intensities of groups of reflections, while intensities of single reflections constitute single observations only when they do not overlap with any other. The final outcome is a set of refined atomic parameters (x,y,z) associated with atomic species. When neutron data are processed parameters of atomic species with negative scattering length can also be determined. If a graphic device is available the user can follow structure solution and refinement on the screen. In the final stage a menu-driven interface is available in order to study molecular geometry and restart refinement. Due to the small ratio "number of observations / number of parameters" the residual R values must be carefully considered by the user (usually final values between 0.06 and 0.20). SOFTWARE ENVIRONMENT: The program has been written in standard Fortran77. A module written in C language is supplied in order to interface the program with X-window or DEC-Window terminal for graphics. Therefore, besides a C compiler, an Xlib library is also needed. Two ASCII files are associated to the program: the first contains coefficients for calculating scattering factors, the second, necessary for graphics, contains on-line help. HARDWARE ENVIRONMENT: The program runs on UNIX and DEC workstations, on mainframe and on personal computers (for this last one 4 Mbytes of RAM and a VGA monitor are needed). PROGRAM SPECIFICATION: The source code of the program consists of 44.000 FORTRAN lines and of 2000 C lines (including comments). DOCUMENTATION: Users instructions and program description (about 1400 lines) are supplied as an ASCII text file. AVAILABILITY: The program is available free of charge from the teams in Bari and in Perugia. A licence agreement has to be signed. REFERENCES Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M.C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27,000-000. Baggio, R., Woolfson, M.M., Declercq, J.P. & Germain, G. (1978). Acta Cryst. A34,883-892. Giacovazzo, C. (1977). Acta Cryst. A33,933-944. Giacovazzo, C. (1980). Acta Cryst. A36,362-372. Main, P. (1978). Acta Cryst. A34,31-38. From pingdu@purisima.molres.org Wed Jan 12 13:49:27 1994 Received: from purisima.molres.org for pingdu@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id MAA08886; Wed, 12 Jan 1994 12:57:19 -0500 Message-Id: <199401121757.MAA08886@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA04058; Wed, 12 Jan 94 09:57:22 -0800 From: ping du Subject: SB Drug Design from a Model Binding Site To: chemistry@ccl.net Date: Wed, 12 Jan 94 9:57:22 PST Cc: pingdu@purisima.molres.org Mailer: Elm [revision: 70.85] Dear Netters, When Xray structures are used for Structure Based Drug Design, a higher than 3 Angstrom resolution is necessary. Are you aware of any examples of SBDD using a model ligand binding site (e.g. from homology modeling)? Ping Du From kallick@nemesis.medc.umn.edu Wed Jan 12 15:49:34 1994 Received: from nemesis.medc.umn.edu for kallick@nemesis.medc.umn.edu by www.ccl.net (8.6.4/930601.1506) id PAA10320; Wed, 12 Jan 1994 15:18:11 -0500 From: Received: by nemesis.medc.umn.edu (920330.SGI/890607.SGI) (for CHEMISTRY@ccl.net) id AA25407; Tue, 12 Jan 71 14:09:45 -0600 Date: Tue, 12 Jan 71 14:09:45 -0600 Message-Id: <7101122009.AA25407@nemesis.medc.umn.edu> To: CHEMISTRY@ccl.net Subject: DIANA 2 pdb? Dear Surfers, I am using a program from the ETH (Guentert at Wuthrich) that will convert a distance geometry file to a pdb-format file. I need to convert to visualize my dg-type output files using BIOSYM software (BIOSYM software won't read it as is. This is the problem: I can read in the coordinate file, but I cannot write it out in ANY other format, whether it be AMBER, DG, or PDB. I must have the syntax wrong, but I have tried many and varied combinations. I will send email to Guentert himself, but right now its 9PM there, so I ask you people in the meanwhile. Thanks very much, Deborah Kallick Deborah Kallick Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455 kallick@nemesis.medc.umn.edu phone 612 626 1962 fax 612 626 4429 From cindy@MSI.COM Wed Jan 12 17:49:30 1994 Received: from paranoid.msi.com.MSI.COM for cindy@MSI.COM by www.ccl.net (8.6.4/930601.1506) id RAA11685; Wed, 12 Jan 1994 17:46:40 -0500 Received: by paranoid.msi.com.MSI.COM (4.1/SMI-4.1) id AA14911; Wed, 12 Jan 94 17:46:04 EST Date: Wed, 12 Jan 94 17:46:04 EST From: cindy@MSI.COM (Cindy Jolly) Message-Id: <9401122246.AA14911@paranoid.msi.com.MSI.COM> To: CTARG@Levels.UniSA.Edu.Au, chemistry@ccl.net Subject: Re: quartz crystal microbalances Hi, The group I worked in as a grad. student had one. The guy that was in charge of it is now at Southwest Research Institute in San Antonio, TX. His name is Dr. Charles Baker. I don't have an e-mail. Cindy Jolly