From dave@carbon.chem.csiro.au Mon May 24 11:36:48 1993 Message-Id: <199305240636.AA03782@shark.mel.dit.csiro.au> Date: Mon, 24 May 93 16:36:48 EST From: (Dr.) Dave Winkler Subject: Materials safety databases etc To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net Does anyone know whether there are databases of materials safety data sheets (MSDS), or something similar, which relate to the safe handling, toxicity etc of organic chemicals. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From rwoods@biop.ox.ac.uk Mon May 24 13:22:43 1993 Date: Mon, 24 May 1993 12:22:43 +0100 From: rwoods@biop.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096CFB6.970541A0.28504@biop.ox.ac.uk> Subject: Searching Protein 3D Structures Dear Netters, In response to Jon Erickson's enquiry, I would like to suggest the program "IDITIS". IDITIS is a relational database for searching protein structures from the Brookhaven Protein Databank. I have not used the program yet myself, but others in the group use it with apparent success. Iditis is distributed by Oxford Molecular Ltd. Their number is (from the U.S.) 011-44-865-784600. Good searching, Rob Woods Robert J. Woods, Ph.D. Glycobiology Institute University of Oxford South Parks Road Oxford, OX1 3QU From koch@organik.uni-erlangen.de Mon May 24 10:48:41 1993 From: Rainer Koch Message-Id: <9305241419.AA11110@derioc1.organik.uni-erlangen.de> Subject: Ca parameters for MNDO ??? To: chemistry@ccl.net Date: Mon, 24 May 93 16:19:02 METDST Fellow netters, does anyone out there has MNDO parameters for Ca? As far as I know there must have been one set maybe 4 or 5 years ago, published by Voityuk in a russian journal. Thanks in advance, Rainer Rainer Koch Inst. f. Organische Chemie Universitaet Erlangen-Nuernberg Henkestr.42 W-91051 Erlangen E-mail: koch@organik.uni-erlangen.de Fax: +49-9131-85-9132 From dobado@ugr.es Mon May 24 16:16:31 1993 Date: Mon, 24 May 1993 16:16:31 UTC+0200 From: Jose Antonio Dobado Subject: Re: Materials safety databases etc. To: chemistry@ccl.net Message-Id: <42*/S=dobado/O=ugr/PRMD=iris/ADMD=mensatex/C=es/@MHS> ----------------------------- Start of body part 1 In the Sigma-Aldrich catalog there is a Material Safety Data Sheets on CD-ROM It includes over 58.000 complete, printable Material Safety Data sheets with chemical structures 500.000 names and synonyms. Features include: Rapid search capability Easy-to-use graphic display Esports structures to WIMP Prints up to 30 different data sheets in one operation Chemical structures displayed with safety data text Export text to over 100 printer models Search fields-Sigma, Aldrich or Fluka catalogue number, CAS registry number, name/synonym, molecular formula System requirements: IBM PC, PC-XT, PC-AT, and PS/2 computers CDROM drive and cable/interface DOS 3.1 or higher 640k RAM (512k available) High Sierra driver** Microsoft mouse (optional) Microsoft MS-DOS extensions for CD-ROM** Hercules monochrome, IBM, CGA, EGA, VGA, or MCGA color graphics Hard disk (required by ALDRICHEM) or 2 floppy drives ** included with CD-Rom cable/interface kits this is the information included in Sigma-Aldrich catalog for more information call international phone 34-1-6619977 I hope this can help you Jose ----------------------------- Start of body part 2 ****************************************************************************** * /\ | Jose Antonio Dobado Jimenez * * / \ | Dept. Quimica Organica * * | G D | Grupo de Modelizacion | Universidad de Granada * * | M M | y Diseno Molecular | 18071 Granada (SPAIN) * * \ / | Tel: + 34 58 243186 * * \/ | Fax: + 34 58 243186 * * | e-mail dobado@ugr.es * ****************************************************************************** ----------------------------- End of body part 2 From stoutepf@lldmpc.dnet.dupont.com Mon May 24 07:12:04 1993 Date: Mon, 24 May 93 11:12:04 -0400 Message-Id: <9305241512.AA10498@esds01.es.dupont.com> From: stoutepf@lldmpc.dnet.dupont.com (Pieter Stouten, +1-302-695-3515) To: "chemistry@ccl.net"@esds01.dnet.dupont.com Subject: RE: Searching Protein 3D Structures On Mon, 24 May 1993 12:22:43 +0100, Rob Woods wrote: >In response to Jon Erickson's enquiry, I would like to suggest the >program "IDITIS". IDITIS is a relational database for searching >protein structures from the Brookhaven Protein Databank. > I am not sure that a strictly relational approach is very effective when searching protein sequence and structure databases since one often is interested in properties of stretches of residues rather than individual residues. In a purely relational system this requires a large number of operations or columns. Permit me to suggest an alternative program. The multi-purpose modelling program WHAT IF incorporates a very fast and flexible database system (SCAN3D), which uses the relational paradigm whenever possible, but also allows for matching of a stretch of residues with a single comparison. For more information, please contact WHATIF's author Gert Vriend directly. He can be reached at vriend@embl-heidelberg.de. Relevant references are: * G. Vriend, "WHAT IF: a molecular modeling and drug design program", J. Mol. Graph., 8, 5255 (1990). * P.F.W. Stouten & G. Vriend, "How to Extract Non-Trivial Information from Protein Structure and Sequence Data: The SCAN3D Retrieval System," Chem. Design Autom. News 7(5) (1992) 18-23. * G. Vriend, C. Sander & P.F.W. Stouten, "A Property-Profile-Oriented Protein Sequence-Structure Database." Submitted for publication. Hope this helps. Cheers, Pieter Stouten The Du Pont Merck Pharmaceutical Company P.O. Box 80353 Wilmington, DE 19880-0353 Phone + 1 - 302 - 695 - 3515 Fax + 1 - 302 - 695 - 2813 E-mail stoutepf@lldmpc.dnet.dupont.com From chm6@midway.uchicago.edu Mon May 24 06:27:47 1993 Date: Mon, 24 May 93 11:27:47 CDT From: "charles h martin" Message-Id: <9305241627.AA19495@midway.uchicago.edu> To: CHEMISTRY@ccl.net Subject: data compression Dear Netters, I am trying to find out if anyone has a data compression subroutine (general or specific) which would allow one to create a binary file with individually compressed records. A sinple routine which can compress an array (real or integer) would do the trick just fine. I will summarize the repsonses. Thanks Chuck Martin ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu U.S. snail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-6853 ================================================================== From jas@medinah.atc.ucarb.com Mon May 24 12:06:33 1993 Message-Id: <9305242107.AA15989@medinah.atc.ucarb.com> Date: Mon, 24 May 1993 17:06:33 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: VSEPR Forcefield This is probably a very old (and abandoned) idea, but let me ask anyway. Has anyone ever tried developing a forcefield based on a simple VSEPR model that has separate terms for all valence electrons? ...that is, having separate sigma and pi bond components and explicitly including nonbonding valence electrons? ...essentially, treating lone pair and p-pi orbitals as pseudoatoms. With the pi bonding components separated out and nonbonding electrons explicitly included, one could use fully repulsive bond angle terms that always had their minimum at 180 degrees (and perhaps only as an augmentation to explicit 1,3 vdW and electrostatic interactions). With such a model, the "ideal" directed geometries would fall out naturally since they would just minimize the angular repulsions. This might also eliminate the need for many atom types since hybridization would be explicitly separated. Pi bonds terms would in general be attractive, with the net effect of shortening double and triple bonds. There would also be new dihedral (or 1,4) terms introduced involving lone pairs and single p-pi electrons (with the p-pi, p-pi interactions very strongly favoring coplanar and perpendicular conformations.) Some questions might be: Would the sigma and pi terms be independently transferable? How does one specify the direction vectors for lone pair and p-pi orbitals? Would most/all lone pair and p-pi orbitals look/act basically alike? (Or specific to an atom type?) If 1,3 vdW and electrostatic interactions are included, is there a universal (tranferable) form for the angular repulsion terms? And, should there be 1,3 terms (vdW and electrostatic) for lone pair and p-pi orbitals? (If so, where would they be centered?) What about unpaired, nonbonded electrons (radicals, diradicals, etc.)? Even more "radical" - can sigma bond terms just be treated as two interacting unpaired electron terms? In fact, can a whole force field be built without explicit bonding, angular or dihedral terms? (A true VSEPR atom-in-molecule approach!) Can electronegativity (chemical potential) equilibration techniques help in deriving such a model where every valence electron is explicitly accounted for? In other words, can they be used to derive orbital-orbital interaction terms instead of atom-atom terms. Could this be extended to delta bonding? Has this horse been beaten to death already? -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From shepard@dirac.tcg.anl.gov Mon May 24 12:09:58 1993 Date: Mon, 24 May 93 17:09:58 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9305242209.AA20571@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: RE: data compression On Mon, 24 May 93 11:27:47 CDT "charles h martin" writes: > I am trying to find out if anyone has a data compression >subroutine (general or specific) which would allow one >to create a binary file with individually compressed records. >A sinple routine which can compress an array (real or integer) >would do the trick just fine. I expect that many people are interested in this. It would be helpful if the methods described in responses to this were characterized according to the following criteria: (1) Lossless or Lossy "Lossless" compression methods allow the original uncompressed data to be reproduced without error, down to the last bit. The unix compress utility is an example. "Lossy" (or is it spelled Lossey?) allows information to be lost in the compression process, but hopefully with some control of the errors. The JPEG image compression is an example. For Lossy methods, the following is important: (2) Absolute or Relative errors Absolute errors are like fixed-point truncations. Each restored number has certain digits that are correct. Relative errors are like floating point truncations. Each restored number has a certain number of digits that are correct. Hopefully, a Lossy method would allow control of one or both of these errors. BTW, I am particularly interested in hearing about Lossy methods of floating point arrays, and lossless methods for integer arrays. -Ron Shepard shepard@tcg.anl.gov From schurko@ccu.UManitoba.CA Mon May 24 12:22:46 1993 Date: Mon, 24 May 1993 17:22:46 -0500 (CDT) From: Robert Schurko Subject: Re: Ca parameters for MNDO ??? To: Rainer Koch Message-Id: On Mon, 24 May 1993, Rainer Koch wrote: > Fellow netters, > > does anyone out there has MNDO parameters for Ca? As far as I know > there must have been one set maybe 4 or 5 years ago, published by Voityuk > in a russian journal. > > Thanks in advance, > Rainer > Try this reference below for a start: C REFERENCE: C "FAST SEMIEMPIRICAL CALCULATIONS", C STEWART. J.J.P., CSASZAR, P., PULAY, P., J. COMP. CHEM., C 3, 227, (1982) and anything else by this same author in J. Comp. Chem. after this date. I also think that the MOPAC program, and for sure GAUSSIAN 92 have full parameter sets. I have the G92 one, but it is in a fortran source, and probably wouldn't mean much. As well, I'm not sure if it's legal, since G92 is no longer a public domain package. Good luck, Rob ============================================================================= schurko@ccu.umanitoba.ca Robert Schurko Chemistry Department (204)-474-9335 University of Manitoba Winnipeg, MB, CANADA =============================================================================