From thomas_w@btm2x2.mat.uni-bayreuth.de Fri Aug 18 03:18:51 1995 Received: from btr0x1.hrz.uni-bayreuth.de for thomas_w@btm2x2.mat.uni-bayreuth.de by www.ccl.net (8.6.10/950810.1506) id DAA16108; Fri, 18 Aug 1995 03:03:03 -0400 Received: from btm2x2.mat.uni-bayreuth.de by btr0x1.hrz.uni-bayreuth.de (4.1/btr0x1 (UBTGW/btr0x1-2.4.7)) id AA08858; Fri, 18 Aug 95 09:02:43 +0200 Received: by btm2x2.mat.uni-bayreuth.de (4.1/SMI-4.1) id AA00142; Fri, 18 Aug 95 09:00:43 +0200 Date: Fri, 18 Aug 95 09:00:43 +0200 From: thomas_w@btm2x2.mat.uni-bayreuth.de (Thomas Wieland) Message-Id: <9508180700.AA00142@btm2x2.mat.uni-bayreuth.de> To: chemistry@www.ccl.net Subject: Summary: Topological indices Dear Netters, here is my summary for my recent question on software for topological indices. It took some time because two weeks ago the mainboard of my computer was stolen such that I didn't have access tothe data on my hard disk (meanwhile I got a new one). Furthermore I have to admit that I hadn't remembered that the same question had been posted this spring (by "Richard Bone" on 22 May 1995 14:45:43 - look for it in CCL archive). The inquiries I received show, however, that the need for information on this topic is not fulfilled yet. Thanks to all scientists who answered. My special thank are due to Dr. S. Basak of Resource Institute, Dulluth, MN, who even sent me a pile of (p)reprints of his works with a lot of valuable information and useful references. It turned out that there is excellent software available - but not public domain. Some simple connectivity or distance indices are certainly not hard to implement and can be looked up in a large number of publications. But some more efforts are needed to program more complex indices. Best regards, Th. Wieland Thomas Wieland +---------------+ Dipl. Math. |+---- +----+| Lehrstuhl II f. Mathematik |\ \ | || Universitaet Bayreuth | \ \ | || | \ \ | || 95440 Bayreuth | \ \\ || Germany | \ \\ || Tel. +49 (921) 553386 | \ \\ || Fax +49 (921) 553385 | \-------|| +---------------+ ------------------------------------------------------------------------------ Original question was: >Dear Colleagues, > >I am looking for some simple programs (preferably public-domain, >best with sources) that are able to compute topological indices >of molecular graphs, no matter which (Wiener-Index, Randic-Index >etc.) > >I would gratefully appreciate any hints to ftp-sites where such software >can be found. I tried some WWW-search machines but my key words "topological >index" didn't suffice. > ------------------------------------------------------------------------------ From: Lipkowitz A great list of programs for computational chemistry is in each Appendix of Reviews in Computational Chemistry, VCH Publishers Inc. The list is prepared by Don Boyd and I'm sure has what you're looking for. Kenny ------------------------------------------------------------------------------ From: "Dr. Subhash Basak" Thank you for your inquiry. We have two programs, POLLY and APPROBE which are currently being used by companies like Upjohn, Glaxo, Government agencies like U S Environmental Protection Agency, National Institutes of Health, US Army for molecular design and QSAR analysis pertaining to health and environment. I am sending you info about POLLY AND APPROBE below. I am also mailing you a collection of my papers in the area of development of topological indices and their applications in QSAR and quantifications of molecular similarity as well as applications of similarity in estimating properties of molecules. The POLLY software is copyright of the University of Minnesota. Licensing/ ordering information regarding POLLY can be obtained from Bob Hicks of the Office of Research and Technology Transfer Administration (ORTTA) of the U of Minnesota. Bob can be reached at: bob@ortta.umn.edu. The price of the software is $2,000.00 (two thousand dollars only) per licensed site. Mr. Hicks can give you more details about the licensing aspects. POLLY v. 2.3 S.C. Basak Natural Resources Research Institute University of Minnesota Duluth, Minnesota 55811 USA D.K. Harriss V.R. Magnuson Department of Chemistry University of Minnesota Duluth, Minnesota 55812 USA !Copyright (C) 1986, 1988 Regents of the University of Minnesota. All Rights Reserved. I. Introduction POLLY is a tested and documented computer program which calculates the values of 98 topological (graph theoretic, connectivity and complexity type) indices for molecules containing up to 120 atoms composed of the following atom types: carbon, nitrogen, oxygen, chlorine, bromine, sulfur, fluorine, phosphorous, iodine, boron and hydrogen. These indices include the Zagreg group indices1 , Wiener index2, Randic's connectivity index3, higher order connectivity indices and valence connectivity indices of different types4, bonding connectivity indices5, information theoretic indices based on distance matrix6, indices of neighborhood symmetry7,8, information theoretic indices of degree complexity, distance complexity and vertex complexity9, information theoretic indices on graph orbits10, and paths of different lengths. Topological indices have been successfully used in the quantification of molecular similarity5, 11-15, structure-property correlations2-4,16-19, and prediction of biomedicinal and toxic properties of different classes of molecules4,7,8,20. The program is structured to accept molecular descriptions in the form of SMILES notation but is easily adapted to other, user oriented, forms of input such as MOLFILE. The output consists of values of the 98 indices for each molecule. POLLY is programmed in ANSI C and has been tested on UNIX and MSDOS platforms. POLLY is provided in source code form only on UNIX platforms, both source and executable for the MSDOS platform. II. Running POLLY POLLY may be run in either interactive (input from the keyboard) or batch (input from a file) modes. To enter input from the keyboard, just type polly at the operating system prompt: Prompt> polly POLLY will then respond with a SMILES: prompt. At this point, type in the SMILES string to specify the compound. The indices, or an error message if an invalid SMILES string, will be output to the console. A sequence number is output as well. This number is just how many compounds POLLY has processed during the current session. The usage of POLLY in batch mode has the following format: Prompt> polly input_name Here input_name is the name of the file with molecule identifiers and SMILES strings (See Sec III for descriptions). The default extension for this file is ".smi" and may be dropped from the command line. If any other extension is used it must be explicitly stated. By default, POLLY will write indices to a file with the same base name as the input file, appending the extension .mci and error messages to a file with the extension .err. For example, if a user runs POLLY with the following command line: polly test.smi indices will be written to test.mci and error messages will be written to test.err. You my override these defaults by specifying the output and error file names on the command line. III. Input A. Format For batch mode, POLLY requires an identifier followed by one or more spaces, and a SMILES21 string (described below). The sequence number and SMILES string must occur on one line. The identifier may be composed of any ASCII character, excluding white space characters and is limited to 80 characters in length. B. SMILES string POLLY uses the SMILES (Simplified Molecular Identification and Line Entry System) method for specifying topological structure of a compound. The structure represented by a SMILES string should, under most circumstances, be hydrogen suppressed. The SMILES interpreter within POLLY will determine the location of hydrogens implicitly by the normal valence of the atoms to which they would be connected. 1. Atom representation Each atom is represented by its atomic symbol. For single letter symbols, use lower case letters to represent aromatic atoms, upper case letters to represent aliphatic atoms. Double letter symbols are represented be an uppercase first letter, lowercase second letter. If you must indicate aromaticity of an atom with a double letter symbol, the symbol should be followed by an "!". Double letter symbols can have ambiguous interpretation. For example, the symbol for silicon, Si, could be interpreted as aliphatic sulfur bonded to aromatic iodine. Any double letter symbol that could have ambiguous interpretation should be enclosed in square brackets "[]". Silicon would then be represented by [Si]. If the double letter symbol would not have ambiguous interpretation, the brackets are not required (e.g. bromine is Br, not [Br]). Examples: Chlorine Cl or [Cl] Silicon [Si] Aliphatic carbon C Aromatic carbon c 2. Bonds By default, the bond between any two atoms is a single bond (see section III.B.4, aromatic rings for an exception). To override this default, the bond must be explicitly represented. The following bond types are available: Single - Double = Triple # Examples: Ethane CC or C-C Ethene C=C Ethyne C#C 3. Branches When an atom has more than two connecting atoms, the additional connecting chains should be enclosed in parentheses. The chain within a set of parentheses is interpreted as being connected to the atom immediately preceding the left parenthesis. You may nest parentheses. Examples: Carbon tetrachloride ClC(Cl)(Cl)Cl Di-n-butylphosphate O=P(OCCCC)OCCCC or CCCCOP(=O)OCCCC Note in the second SMILES string for Di-n-butylphosphate the double bond to the oxygen is also enclosed within the parentheses. Any bonding information to an atom within parentheses must also be enclosed within the parentheses. 4. Rings To represent a ring as a linear structure, one bond in the ring must be broken. This structure can then be represented as a linear string. To identify where the broken bond occurred, each atom that was involved is labeled with a digit(s). These two atoms comprise a ring-closure pair. The digit is placed following the two atoms that had the bond broken between them. The interpreter may then re-establish the bond in the connection matrix. Two digits may be used to identify ring-closure pairs if they are preceded by the character "%". Therefore, up to 99 (1-99) rings may be labeled. Examples: Cyclohexane C1CCCCC1 1-Methylcyclopentene CC%11=CCCC%11 Aromatic ring: SMILES notation allows atoms in aromatic rings to be represented with lower case atomic symbols. This avoids having to designate conjugated double bonds in aromatic rings, i.e. the default is not a single bond, but the conjugated double bond. Examples: Benzene c1ccccc1 Naphthalene c1cc2ccccc2cc1 5. Atom Qualifiers Placing square brackets around an atom symbol allows you to specify additional information about an atom that can not be implicitly deduced from the connection table. This would include formal charges or hydrogens about an aromatic nitrogen. Examples: Pyrrole c1cccc[nH]1 Tetramethylammonium C[N+](C)(C)C 6. Restrictions a. POLLY utilizes only a subset of all possible atoms, those that allow the representation of most organic compounds. b. The maximum SMILES string length is 120. c. The maximum number of atoms for any compound is 120. d. Only compounds that can be represented by a connected graph are allowed. e. Hydrogens should not be included in the SMILES string except as qualifiers. IV. Output Appendix 1 describes the indices output by POLLY. The order the indices are listed corresponds to the order in which they are output by POLLY. Appendix 2 lists the parameters output on a record by record basis. V. References 1. I. Gutman, B. Ruscic, N. Trinajstic and C. F. Wilcox, Jr., Graph theory and molecular orbitals, Part XII. Acyclic polyenes. J. Chem. Phys., 62, 3339-3405 (1975). 2. H. Wiener, Structural determination of paraffin boiling points, J. Amer. Chem. Soc., 69, 17-20 (1947). 3. M. Randic', On characterization of molecular branching, J. Am. Chem. Soc. 97, 6609-6615 (1975). 4. L.B. Kier and L.H. Hall, Molecular Connectivity in Structure-Activity Analysis (Research Studies Press, Letchworth, Hertfordshire, U.K., 1986). 5. S.C. Basak, V.R. Magnuson, G.J. Niemi and R.R. Regal, Determining structural similarity of chemicals using graph-theoretic indices, Discrete Applied Mathematics, 19, 17 (1988); Special Volume: Applications of Graph Theory in Chemistry and Physics, J.W. Kennedy and L.V. Quintas (eds.). 6. D. Bonchev and N. Trinajstic, Information theory, distance matrix and molecular branching, J. Chem. Phys., 67, 4517-4533 (1977). 7. A.B. Roy, S.C. Basak, D.K. Harriss and V.R. Magnuson, Neighborhood Complexities and Symmetry of Chemical graphs and their biological applications, in Mathematical Modelling in Science and Technology, X.J.R. Avula, R.E. Kalman, A.I. Lipais and E.Y. Rodin (Eds.), p. 745, Pergamon Press, 1984. 8. S.C. Basak, Use of molecular complexity indices in predictive pharmacology and toxicology: a QSAR approach, Med. Sci. Res., 15, 605 (1987). 9. C. Raychaudhury, S.K. Ray, J.J. Ghosh, A.B. Roy and S.C. Basak, Discrimination of isomeric structures using information-theoretic topological indices, J. Comput. Chem., 5, 581 (1984). 10. N. Rashevsky, Life, information theory and topology, Bull. Math. Biophys., 17, 229-235 (1955). 11. M. Randic', in: Computer Based Methods of Molecular Similarity, ed. G.M. Maggiora (John Wiley, in press, 1989). 12. S.C. Basak, V.R. Magnuson, G.J. Niemi, R.R. Regal and G.D. Veith, Topological indices: their nature, mutual relatedness, and applications, Mathematical Modelling, 8, 300 (1987). 13. M. Johnson, S.C. Basak and G. Maggiora, A characterization of molecular similarity methods for property prediction, Mathematical and Computer Modelling, II, 630 (1988). 14. M. Lajiness, Molecular Similarity Based Methods for Selecting compounds for Screening, in: Computational Chemical Graph Theory, Ed. D. H. Rouvray, Nova, New York. pp. 299-316 (199). 15. S.C. Basak, S. Bertelsen and G.D. Grunwald, Application of graph theoretic parameters in quantifying molecular similarity and structure-activity relationships, presented at the Fifth International Conference on Mathematical Chemistry (1993). 16. S.C. Basak and G.D. Grunwald, Use of graph invariants, volume and total surface area in predicting boiling point of alkanes, Mathematical Modelling and Scientific Computing, 2, 735-740 (1993). 17. S.C. Basak, G.J. Niemi and G.D. Veith, Optimal characterization of structure for prediction of properties, J. Math. Chem., 4, 185 (1990). 18. Basak, S.C. A Nonempirical Approach to Predicting Molecular Properties using Graph-Theoretic Invariants, in PRACTICAL APPLICATIONS OF QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSAR) IN ENVIRONMENTAL CHEMISTRY AND TOXICOLOGY, eds. W. Karcher and J. Devillers, Kluwer Academic Publishers, (1990). 19. G.J. Niemi, S.C. Basak, G.D. Veith and G. Grunwald, Prediction of octanol- water partition coefficient (Kow) using algorithmically-derived variables, Environmental Toxicology and Chemistry, 11, 893-900 (1992). 20. G.J. Niemi, S.C. Basak and G.D. Veith, A theoretical and computational approach to chemical evaluation based on structure-activity relationships, Procedeedings of the First Conference of the International Society of Environmental Protection, pp 57-68 (1990). 21. E.B. Anderson, G.D. Veith, and D. Weininger, SMILES: A Line notation and computerized interpreter for chemical structures, Environmental Research Brief, U.S. EPA, (1987). ! Appendix 1: The 98 topological indices calculated by POLLY. IWD Information index for the magnitudes of distances between all possible pairs of vertices of a graph IWD Mean information index for the magnitude of distance W Wiener index = half-sum of the off-diagonal elements of the distance matrix of a graph ID Degree complexity HV Graph vertex complexity HD Graph distance complexity IC Information content of the distance matrix partitioned by frequency of occurrences of distance h O Order of neighborhood when ICr reaches its maximum value for the hydrogen-filled graph IORB Information content or complexity of the hydrogen-suppressed graph at its maximum neighborhood of vertices OORB Maximum order of neighborhood of vertices for IORB within the hydrogen- suppressed graph M1 A Zagreb group parameter = sum of square of degree over all vertices M2 A Zagreb group parameter = sum of cross-product of degrees over all neighboring (connected) vertices ICr Mean information content or complexity of a graph based on the rth (r = 0..6) order neighborhood of vertices in a hydrogen-filled graph SICr Structural information content for rth (r = 0..6) order neighborhood of vertices in a hydrogen-filled graph CICr Complementary information content for rth (r = 0..6) order neighborhood of vertices in a hydrogen-filled graph h! Path connectivity index of order h = 0..6 h!C Cluster connectivity index of order h = 3..6 h!Ch Chain connectivity index of order h = 3..6 h!PC Path-cluster connectivity index of order h = 4..6 h!b Bonding path connectivity index of order h = 0..6 h!bC Bonding cluster connectivity index of order h = 3..6 h!bCh Bonding chain connectivity index of order h = 3..6 h!bPC Bonding path-cluster connectivity index of order h = 4..6 h!v Valence path connectivity index of order h = 0..6 h!vC Valence cluster connectivity index of order h = 3..6 h!vCh Valence chain connectivity index of order h = 3..6 h!vPC Valence path-cluster connectivity index of order h = 4..6 Ph Number of paths of length h = 0..10 ! Appendix 2: Format of the POLLY output file Record 1: Chemical id (a80) Record 2: IWD, IWD, W, ID, HV, HD, IC (f11.3, f8.3, i6, 4f8.3) Record 3: O, IORB, OORB, M1, M2 (i6, f8.3, 3i6) Record 4: IC0, IC1, ..., IC6 (7f8.3) Record 5: SIC0, SIC1, ..., SIC6 (7f8.3) Record 6: CIC0, CIC2, ..., CIC6 (7f8.3) Record 7: 0!, 1!, ..., 6! (7f8.3) Record 8: 3!C, 4!C, 5!C, 6!C (24x, 4f8.3) Record 9: 3!Ch, 4!Ch, 5!Ch, 6!Ch (24x, 4f8.3) Record 10: 4!PC, 5!PC, 6!PC (32x, 3f8.3) Record 11: 0!b, 1!b, ..., 6!b (7f8.3) Record 12: 3!bC, 4!bC, 5!bC, 6!bC (24x, 4f8.3) Record 13: 3!bCh, 4!bCh, 5!bCh, 6!bCh (24x, 4f8.3) Record 14: 4!bPC, 5!bPC, 6!bPC (32x, 3f8.3) Record 15: 0!v, 1!v, ..., 6!v (7f8.3) Record 16: 3!vC, 4!vC, 5!vC, 6!vC (24x, 4f8.3) Record 17: 3!vCh, 4!vCh, 5!vCh, 6!vCh (24x, 4f8.3) Record 18: 4!vPC, 5!vPC, 6!vPC (32x, 3f8.3) Record 19: P0, P1, ..., P10 (11i6) ------------------------------------------------------------------------ From: lnl@novo.dk (Leif Norskov) Molconn-X is *THE* program for calculating topological indices. ( - sometimes referred to as Kier and Hall indices). It is available for $ 295 for academic users from Lowell H. Hall Hall Associates Consulting 2 Davis Street Quincy, MA 02170, U.S.A. Tel. (617) 773-4833 Lowell does not seem to have an email address, but he certainly does put some nice stamps on his ordinary mail :-) ------------------------------------------------------------------------ From: "Igor Baskin" In connection with your inquiry about topological indexes, I enclose a small extraction from the description of the EMMA package. "EMMA" ("EFFECTIVE MODELLING OF MOLECULAR ACTIVITY") - THE SOFTWARE FOR THE PREDICTION OF PROPERTIES/BIOLOGICAL ACTIVITIES OF ORGANIC COMPOUNDS ON THE BASIS OF REGRESSION ANALYSIS ... For each structure in a training set EMMA allows to compute from hundreds to thousands of descriptors. The set of descriptors includes topological indices (various connectivity indices, Balaban index J, Wiener and extended Wiener, Hosoya, Merrifield-Simmons, Gutman and some other indices), informational indices, the indices which are the functions of charge distribution in molecules, the indices based on atomic electronegativities and those based on inductive parameters, steric indices, various local indices and, what is important, the substructural descriptors which are equal to the number of chaines (1- to 9-atomic), the number of cycles (3- to 6-membered) and the number of branched fragments (4-, 5-, and 6-atomic), the atoms in substructures being classified taking into account the number of hydrogens at them, bond types and formal charge. EMMA can manage 2000 descriptors computed and construct the regression equations including only a few "best" descriptors. A user can easily add his own descriptor programs or can input the additional descriptor values manually. ... Developers: Professor N.S.Zefirov, Department of Chemistry, Moscow State University, Moscow, 119899, Russia. Fax: (095) 939-0290, phone (095) 939-1620 Dr. D.V.Sukhachev, Dr. I.I.Baskin, Dr. V.A.Palyulin From noy@tci002.uibk.ac.at Fri Aug 18 05:03:52 1995 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.10/950810.1506) id FAA17280; Fri, 18 Aug 1995 05:00:45 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA01353 (5.65c/IDA-1.4.4 for ); Fri, 18 Aug 1995 11:00:26 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA30680; Fri, 18 Aug 1995 11:00:25 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9508180900.AA30680@tci002.uibk.ac.at> Subject: Biosym/MSI combination To: chemistry@www.ccl.net Date: Fri, 18 Aug 1995 11:00:25 +0200 (DFT) In-Reply-To: <9508171824.AA05385@ucmod2.che.uc.EDU> from "Jeffrey L. Nauss" at Aug 17, 95 02:24:34 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2427 : I am assuming that most people are aware of the merger between Biosym : and MSI. When I heard of that I immediately had some concerns which I : would like to share with you. Hi ! I would like to share some issues. I don't think the merger will create a big impact to the molecular modeling society but I still put some doubts on whether the companies are facing financial problems rather than to promote growth ? : 1) Pricing of software - we will now have a single company owning the : two largest software pacakages in at least North America (or pretty : close to it). Competition will be reduced and that usually means : prices will go up. The price will not go up that much if the merging leads to cost-efficiency. Especially, I still hope that it will not affect the academia. I have been witnessing many free software for molecular modeling appearing more frequently. This gives a sign that competition is not low enough for the new company to deviate the price from the demand/supply law. : 4) Will the reduced competition diminish the incentive to improve the : software? - Could the corporate attitude found at large companies like : IBM dominate Biosym/MSI so that improvements and innovations are made : grudingly, sporatically, and not in touch with customer desires? : Healthy competition usually means better products. As I see it, that : competition is significantly reduced. So what incentive is there for : continued product development? Biosym already has a reputation (at : least in my circle of aquintances) as being somewhat buggy. What will : happen now? The merging may help improve the development of softwares. Many overlap of works in the two companies can be eliminated and many new areas can be explored using the advantage of exceeding staffs. I think it is just a question of the new management, how good they can administrate the new company. I just regard the change as an disappearance of one company. The market is still highly competitive. take care, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen E-mail: noy@tci2.uibk.ac.at (University of Innsbruck) Homepage http://www-c724.uibk.ac.at/noy/ Phone (43)(512) 507-5163 Research: computer-aided molecular design ----------------------------------------------------------------------------- From dimitris@3dp.com Fri Aug 18 08:03:54 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/950810.1506) id IAA18820; Fri, 18 Aug 1995 08:01:12 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA23077; Fri, 18 Aug 95 08:05:33 -0400 Received: by europa.3dp.com (931110.SGI) id AA13754; Fri, 18 Aug 95 08:02:46 -0400 From: "Dimitris Agrafiotis" Message-Id: <9508180802.ZM13752@europa.3dp.com> Date: Fri, 18 Aug 1995 08:02:45 -0400 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Re: Biosym/MSI merger Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Aug 17, 10:01pm, Keith Refson wrote: > The question that immediately sprang to my mind on reading about the > Biosym/MSI merger is "why?". What is the motivation for the two most > direct competitors in this field to combine? In plain english, it's called selection by elimination. 'Merger' is a synonym used by business executives. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From dave@wh.bayer.com Fri Aug 18 08:33:55 1995 Received: from wh.bayer.com for dave@wh.bayer.com by www.ccl.net (8.6.10/950810.1506) id IAA19053; Fri, 18 Aug 1995 08:33:13 -0400 From: Received: from mrcs1 ([140.250.41.24]) by wh.bayer.com (8.6.12/8.6.12) with SMTP id IAA13231 for ; Fri, 18 Aug 1995 08:30:22 -0400 Received: by mrcs1 (5.64/X1.00) id AA18945; Fri, 18 Aug 95 08:30:38 -0400 Date: Fri, 18 Aug 95 08:30:38 -0400 Message-Id: <9508181230.AA18945@mrcs1> To: chemistry@www.ccl.net Subject: Re: Mg++2 parameters I recently asked a question about MM parameters for Mg++2. Many thanks to all who responded. The consensus is that the best are in: J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J. Phys. Chem. (1990), 94, 8021-8024. However, be warned if you do a CAS search on Aqvist (as I did at the start of all this) the name is mispelled as Aaqvist for this particular paper, proving once again that our answers are only as good as our databases..... p.s. If anyone from CAS is watching, feel free to correct this error. Dave ---------------------------------------------------------------- David Hartsough dave@wh.bayer.com Structural Chemistry Bayer Research Center 400 Morgan Lane Phone: (203)937-2982 West Haven CT 06516 Fax: (203)937-2650 ---------------------------------------------------------------- The opinions expressed herein are solely those of the author and are not necessarily those of Bayer ---------------------------------------------------------------- From jtgolab@amoco.com Fri Aug 18 09:33:56 1995 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.6.10/950810.1506) id JAA19738; Fri, 18 Aug 1995 09:26:17 -0400 Received: by interlock.amoco.com id AA10388 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Fri, 18 Aug 1995 08:26:13 -0500 Message-Id: <199508181326.AA10388@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Fri, 18 Aug 1995 08:26:13 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Fri, 18 Aug 1995 08:26:13 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Fri, 18 Aug 1995 08:26:13 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Fri, 18 Aug 1995 08:22:43 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: RE: Concerns with the Merger Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 >> Keith Refson wrote: >> [Parts of Original Message Edited/Deleted] << > The question that immediately sprang to my mind on reading about the > Biosym/MSI merger is "why?". We speak of Biosym and MSI as if they are still companies; all of us should notice that Corning now owns almost all of the major molecular modeling software in the world. That is the scary part in my opinion. DISCLAIMER: All of this stuff is an opinion of my own conception. Any resemblance to company policy is entirely coincidental and completely in the mind of the reader. -- :Joe jtgolab@amoco.com (708) 961-7878 +-------------------------------------------------------------------------+ | There are two kinds of people, those who finish what they start and ... | | - Robert Byrne | +-------------------------------------------------------------------------+ From craig@occam.gh.wits.ac.za Fri Aug 18 10:03:57 1995 Received: from occam.gh.wits.ac.za for craig@occam.gh.wits.ac.za by www.ccl.net (8.6.10/950810.1506) id KAA20316; Fri, 18 Aug 1995 10:00:35 -0400 Received: (from craig@localhost) by occam.gh.wits.ac.za (8.6.12/8.6.9) id PAA10899; Fri, 18 Aug 1995 15:53:09 +0200 Date: Fri, 18 Aug 1995 15:53:09 +0200 (GMT+0200) From: Craig Taverner X-Sender: craig@occam.gh.wits.ac.za To: Dimitris Agrafiotis cc: chemistry@www.ccl.net Subject: Re: CCL:Biosym/MSI merger In-Reply-To: <9508180802.ZM13752@europa.3dp.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 18 Aug 1995, Dimitris Agrafiotis wrote: > On Aug 17, 10:01pm, Keith Refson wrote: > > The question that immediately sprang to my mind on reading about the > > Biosym/MSI merger is "why?". What is the motivation for the two most > > direct competitors in this field to combine? > > In plain english, it's called selection by elimination. 'Merger' is a > synonym used by business executives. Despite the obscure way it was written, I got the distinct impression it was a case of biosym (ie. it's parent company) buying out MSI. Perhaps I'm wrong, but it certainly sounded like that to me. If it is the case, then it's the kind of 'competition' I'd expect to lead to higher prices. Let's all support the public domain ;-) "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa From kotelyan@che.udel.edu Fri Aug 18 10:15:57 1995 Received: from che.udel.edu for kotelyan@che.udel.edu by www.ccl.net (8.6.10/950810.1506) id JAA20276; Fri, 18 Aug 1995 09:57:11 -0400 Received: by che.udel.edu (AIX 3.2/UCB 5.64/4.03) id AA17140; Fri, 18 Aug 1995 09:52:32 -0400 Date: Fri, 18 Aug 1995 09:51:49 +22305241 (EDT) From: Mike Kotelyanski Subject: Re: CCL:Biosym/MSI merger To: Dimitris Agrafiotis Cc: chemistry@www.ccl.net In-Reply-To: <9508180802.ZM13752@europa.3dp.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII So, who is selected and who is eliminated? Michael Kotelyanskii PhD Department of Chemical Engineering University of Delaware kotelyan@che.udel.edu Newark DE 19716 > In plain english, it's called selection by elimination. 'Merger' is a > synonym used by business executives. > > > -- > Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com > Principal Research Scientist | tel: (610) 458-6045 > 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 > 665 Stockton Drive, Suite 104 > Exton, PA 19341 > > > > > -------This is added Automatically by the Software-------- > -- Original Sender From: Address: dimitris@3dp.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From srheller@origin.gig.usda.gov Fri Aug 18 10:49:00 1995 Received: from origin for srheller@origin.gig.usda.gov by www.ccl.net (8.6.10/950810.1506) id KAA21286; Fri, 18 Aug 1995 10:47:05 -0400 Received: by origin (5.x/SMI-SVR4) id AA03151; Fri, 18 Aug 1995 10:46:28 -0400 Date: Fri, 18 Aug 1995 10:46:27 -0400 (EDT) From: "Stephen R. Heller" To: Craig Taverner Cc: Dimitris Agrafiotis , chemistry@www.ccl.net Subject: Re: CCL:Biosym/MSI merger In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It would seem to me the basic reason for the merger is both compnaies are not profitable and the merger may improve their financial situation. The issues of a monopoly and potentailly higher prices for their software and maintenance is another isssue. Steve Steve Heller, USDA, ARS, Plant Genome Program Bldg. 005, Room 337 Beltsville, MD 20705-2350 E-Mail: srheller@nalusda.gov Phone: 301-504-6055 FAX: 301-504-6231 From dimitris@3dp.com Fri Aug 18 11:33:58 1995 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.6.10/950810.1506) id LAA22271; Fri, 18 Aug 1995 11:24:29 -0400 Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA23593; Fri, 18 Aug 95 11:28:48 -0400 Received: by europa.3dp.com (931110.SGI) id AA14184; Fri, 18 Aug 95 11:26:01 -0400 From: "Dimitris Agrafiotis" Message-Id: <9508181126.ZM14182@europa.3dp.com> Date: Fri, 18 Aug 1995 11:26:00 -0400 In-Reply-To: Craig Taverner "CCL:Biosym/MSI merger" (Aug 18, 3:53pm) References: X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Re: Biosym/MSI merger Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Aug 18, 3:53pm, Craig Taverner wrote: > Subject: CCL:Biosym/MSI merger > > Despite the obscure way it was written, I got the distinct impression it > was a case of biosym (ie. it's parent company) buying out MSI. > Perhaps I'm wrong, but it certainly sounded like that to me. > If it is the case, then it's the kind of 'competition' I'd expect to lead > to higher prices. I hate to waste the bandwidth, but who is buying out whom can be infered by the name and previous title of the new CEO. Business executives obey the same laws as the rest of the species on this planet, one of which is survival. I think we should let the dust settle for a while and revist the subject later; maybe after the 'restructuring'. Finally, I don't know much about materials, but, at least in the life sciences, I don't think the world as we know it will cease to exist as a consequence of this transaction. -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From states@rucola.wustl.edu Fri Aug 18 11:39:57 1995 Received: from wugate.wustl.edu for states@rucola.wustl.edu by www.ccl.net (8.6.10/950810.1506) id LAA22323; Fri, 18 Aug 1995 11:26:51 -0400 Received: from rucola (rucola.wustl.edu [128.252.122.177]) by wugate.wustl.edu (8.6.12/8.6.11) with ESMTP id KAA10060; Fri, 18 Aug 1995 10:26:50 -0500 Received: by rucola (950215.SGI.8.6.10/930416.SGI) id KAA12587; Fri, 18 Aug 1995 10:26:41 -0500 From: states@rucola.WUStL.EDU (David J. States) Message-Id: <9508181026.ZM12585@rucola.wustl.edu> Date: Fri, 18 Aug 1995 10:26:41 -0500 In-Reply-To: nauss@ucmod2.che.uc.edu (Jeffrey L. Nauss) "CCL:Question about Electrostatics in Molecular Mechanics" (Aug 4, 12:17pm) References: <01HTN5UE7QKI9OCUY2@SLVAXA.UMSL.EDU> <9508041617.AA04753@ucmod2.che.uc.EDU> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: nauss@ucmod2.che.uc.edu, chemistry@www.ccl.net Subject: Re: CCL:Question about Electrostatics in Molecular Mechanics Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 I worte: >So if you really want to do the calculation correctly, >electronic polarization, in addition to molecular reorientation, must >be modeled explicitly. and Jeffrey L. Nauss responded: ... > However, I am not familiar with > any empirical potential energy function that incorporates polarization > except for that developed in Wilma Olson's group for nucleic acids ... Sorry for the delay in replying. There have been a few empirical potentials published over the years with polarization terms. Adler has done some noble gas simulations and solvation of charged species in noble/vdW gasses and liquids with models that incorporate polarization. There is an ancient (early 70's) Stillinger water model that treated water as a gas of protons and polarizable oxygens (interesting concept, but the resulting model had some problems with fitting experimental data). There is a second polarizable water model from the same era for which I don't recall the authors (it was a Nature article and focused on hydrogen bonding in liquid water). Peter Kolman has also published a polarizable water model (J. Chem. Phys., ? early 80's). Since this is not a field in which I am currently active, there may well have been other, more recent, contributions to the literature. The attraction of such models is that hydrogen bonding falls out in a very natural way as 1/R**4 charge induced dipole and 1/R**6 dipole induced dipole terms. There seem to have been two major stumbling blocks to acceptance of these models. The first is compute time. As part of every PE evaluation, you need to do an iteration to self-consistency for the polarization terms. Even though this iteration usually converges pretty quickly, it multiplies the compute time for a simulation by a factor or 3 to 10. But now that the PC or Mac that you use of wordprocessing is a hundred times faster than the VAX-11/780 on which we ran the original protein molecular dynamics, I don't find this much of an excuse. The second, and perhaps more signficant, problem is one of parameterization. It is clear that bonds and delocalized pi orbital systems have anisotropic polarizations. So you need 6 polarization parameters for every type of bond in a model. For a typical biomolecule, specifying all of these accurately is a pretty duanting task. Hence the focus on water models and monoatomic gases. As long as we are talking about electrostatics, let me get on another soap box: titrable groups. Essentially all biological macromolecules exists as an equilibrium population of different titration states. MD simulations based on a particular assignment of charges (or even uniformly scaled charges) will be fundamentally flawed. It would be interesting to see someone pickup the Stillinger proton/oxygen gas model for water again. The appeal of this approach is that the protons are free to move from site to site so titration can be realistically included in the simulation. This is, afterall, a well documented phenomenon occuring in aqueous solution on a picosecond time scale. David -- David J. States Institute for Biomedical Computing / Washington University in St. Louis From jkl@ccl.net Fri Aug 18 12:18:58 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id MAA23580; Fri, 18 Aug 1995 12:10:49 -0400 Received: from xr1.atlas.fr for Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr by bedrock.ccl.net (8.6.10/930601.1506) id MAA15480; Fri, 18 Aug 1995 12:10:45 -0400 From: X400-Received: by /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Fri, 18 Aug 1995 18:10:02 +0200 X400-Received: by mta xr1.atlas.fr in /PRMD=INTERNET/ADMD=ATLAS/C=FR/; Relayed; Fri, 18 Aug 1995 18:10:02 +0200 X400-Received: by /ADMD=ATLAS/C=FR/; Relayed; Fri, 18 Aug 1995 18:10:13 +0200 X400-Received: by /PRMD=RP/ADMD=ATLAS/C=FR/; Relayed; Fri, 18 Aug 1995 20:01:23 +0200 Date: Fri, 18 Aug 1995 20:01:23 +0200 X400-Originator: Jean-Dominique.J.D.GUITTON@VITRY.RPR/RD/CRVA/BIOTECH.RP-RORER.rp.fr X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 950818180120438241] X400-Content-Type: P2-1984 (2) Content-Identifier: homology modelin Alternate-Recipient: Allowed Message-ID: <"SSWA 950818180120438241*/I=JD/G=Jean-Dominique/S=GUITTON/OU=VITRY/OU=RPR$/RD$/CRVA$/BIOTECH/O=RP-RORER/PRMD=RP/ADMD=ATLAS/C=FR/"@MHS> To: "X400 -CHEMIOSC *?:CHEMISTRY" Subject: homology modeling package I have recently heard about Modeler from MSI, have you still used this software and do you have any comments ? Thanks Dom Jean-Dominique Guitton Rhone Poulenc Rorer Central Research France e-mail: jean-dominique.guitton@rp.fr From jkl@ccl.net Fri Aug 18 12:48:59 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id MAA23949; Fri, 18 Aug 1995 12:35:45 -0400 Received: from hrz-sun1.hrz.uni-kassel.de for gdanitz@hrz.uni-kassel.de by bedrock.ccl.net (8.6.10/930601.1506) id MAA16007; Fri, 18 Aug 1995 12:34:54 -0400 Received: from hrz-serv1.hrz.uni-kassel.de by hrz-sun1.hrz.uni-kassel.de (4.1/SMI-4.1) id AA19695; Fri, 18 Aug 95 18:34:28 +0200 Received: by hrz-serv1.hrz.uni-kassel.de (AIX 3.2/UCB 5.64/HRZ-GhK/HRZ-SERV1/pm) id AA21649; Fri, 18 Aug 1995 18:34:46 +0200 From: gdanitz@hrz.uni-kassel.de (Robert Gdanitz) Message-Id: <9508181634.AA21649@hrz-serv1.hrz.uni-kassel.de> Subject: Num. stability of 4-index transf. in CI To: chemistry@ccl.net (Computational Chemistry List) Date: Fri, 18 Aug 1995 18:34:45 +0200 (MES) +-----+ Robert J. Gdanitz email: gdanitz@hrz.uni-kassel.de | GhK | Gesamthochschule Kassel Tel.: +(49) 561-804-4120 | | Fachbereich 18 (Physik) Fax: +(49) 561-804-4006 +-----+ 34109 Kassel X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 2381 Dear Netters: In CI-calculations one faces the problem of transforming 2e-integrals over (primitive) basis functions (ij|g|kl) to an atomic or a molecular orbital basis yielding (IJ|g|KL) via the (in)famous 4-index transformation (IJ|g|KL) = Sum i,j,k,l U(i,I) * U(j,J) * U(k,K) * U(l,L) * (ij|g|kl) Clearly, numerical stability problems are to be expected if the orbital expan- sion coefficients U "oscillate" with an amplitude that reaches the value of the 4-th root of the reciprocal floating point accuracy, i.e. approx. 1000 in REAL*8. Unfortunately this value (corresponding to a condition number of 1.0E8 of the overlap matrix in the primitive basis set) is quickly reached in the case of a) rather large basis sets, b) diffuse functions for molecules or c) a low or even absent symmetry of the system under investigation and the results may be spurious states that mix with the one to be optimized or even states with almost arbitrary negative values in energy. A few possible solutions that spontaneously came to my mind: * Promoting everything to REAL*16 might be accurate enough to yield numerical stability, however, REAL*16 is not well supported by computer manufacturers and its usage may easily cause a degradation in performance of orders of magnitude (on our SG Power-Challenge, a test program computing dot-products of two vectors was 350 times slower than in REAL*8!) * Only accumulating the partial sums in REAL*16 might help, however, this is, where almost all numerical work is performed, so it should not be much faster than doing everything in REAL*16. In terms of stability, this option should be worse compared to the first, however, it is implemented much easier. * Accumulating the partial sums in the order of descending absolute magnitude increases CPU-time by a constant factor, depending on the algorithm used for the ranking/sorting. The benefits and drawbacks seem to be similar to option two. Unfortunately it seems to be impossible to create a significant (and small) test-case such that a primitive program could be used to find the best solution. I would like to encourage anyone who has comments or suggestions, especially those, who already have experience with performing integral transformations in relatively large basis sets, to write me! If there is enough interest, I will summarize. R. Gdanitz From jkl@ccl.net Fri Aug 18 13:18:59 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950810.1506) id NAA24625; Fri, 18 Aug 1995 13:15:22 -0400 Received: from gatekeeper.tripos.com for mac@metis.tripos.com by bedrock.ccl.net (8.6.10/930601.1506) id NAA16799; Fri, 18 Aug 1995 13:15:03 -0400 Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id MAA01291 for ; Fri, 18 Aug 1995 12:14:10 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma001289; Fri Aug 18 12:14:04 1995 Received: from metis.UUCP (metis.tripos.com [192.160.145.41]) by tripos.tripos.com (8.6.12/8.6.12) with SMTP id MAA09560; Fri, 18 Aug 1995 12:11:44 -0500 Received: by metis.UUCP (4.0/4.7) id AA13005; Fri, 18 Aug 95 10:11:22 PDT Message-Id: <9508181711.AA13005@metis.UUCP> To: chemistry@ccl.net Cc: mike@tripos.tripos.com, schwartz@tripos.tripos.com Subject: Tripos on World Wide Web Date: Fri, 18 Aug 95 12:11:21 EDT From: "Malcolm A. Cline" Tripos, Inc. would like to announce its presence on the Internet. The Tripos Home Page can be found at URL: http://www.webcom.com/~tripos2/ This address will probably change over the next few months as we reconcile our two domain names. Take a look at What's New at Tripos. Interesting reading! mac@tripos.com Malcolm A. Cline WebMaster Tripos, Inc. From landin@membrana.mednet.gu.se Fri Aug 18 18:19:01 1995 Received: from mailer.gu.se for landin@membrana.mednet.gu.se by www.ccl.net (8.6.10/950810.1506) id SAA03604; Fri, 18 Aug 1995 18:10:40 -0400 Received: from membrana.mednet.gu.se (membrana.mednet.gu.se [130.241.71.23]) by mailer.gu.se (8.6.10/8.6.10) with ESMTP id AAA12256; Sat, 19 Aug 1995 00:10:34 +0200 Received: by membrana.mednet.gu.se (940816.SGI.8.6.9/940406.SGI.AUTO) id AAA04176; Sat, 19 Aug 1995 00:11:14 +0200 From: "Johan Landin" Message-Id: <9508190011.ZM4174@membrana.mednet.gu.se> Date: Sat, 19 Aug 1995 00:11:08 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: CCL: RE PM3 for phosphates Cc: landin@clavicula.mednet.gu.se, dave@wh.bayer.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Does anyone have any info regarding the > accuracy of PM3 for phosphates (in particular > ATP but any phosphate will do)? I have looked > in JCC 10 (1989) 221-264 and cannot seem to > find anything regarding this. Any info would > be greatly appreciated.... We have recently investigated this for the case of the dimethylphosphate anion and found that PM3 was unable to describe the conformational energy surface correctly. See Landin, J., Pascher, I. & Cremer, D. Journal of Physical Chemistry 99, 4471-4485 (1995). which also gives an explanation to the PM3 failure. Anyone interested in a reprint should send an e-mail request. Regards /Johan _______________________________________________________________ Johan Landin Tel: +46 31 773 3767 Dept. of Medical Biochemistry Fax: +46 31 41 6108 Medicinaregatan 9 Home: +46 31 14 7554 S-413 90 Goteborg, Sweden Email: landin@mednet.gu.se From martin.norin@sto.pharmacia.se Fri Aug 18 19:19:02 1995 Received: from gatekeeper.pharmacia.se for martin.norin@sto.pharmacia.se by www.ccl.net (8.6.10/950810.1506) id TAA03992; Fri, 18 Aug 1995 19:11:42 -0400 Received: from mailgate.pharmacia.se by gatekeeper.pharmacia.se; (5.65/1.1.8.2/16Feb95/sal) id AA16189; Sat, 19 Aug 1995 01:15:42 +0200 Received: by mailgate.pharmacia.se (5.65/DEC-Ultrix/4.3/sal-950131) id AA12543; Sat, 19 Aug 1995 01:08:05 +0200 Date: Sat, 19 Aug 1995 01:08:05 +0200 Received: from umc by mailgate.pharmacia.se via MR/PHAROS with conversational-MRIF; Sat, 19 Aug 95 01:08:05 +0200 Posted: Sat, 19 Aug 95 01:02:29 +0200 Sender: martin.norin@sto.pharmacia.se From: "NOYM" Message-Id: <2028020119081995/A02131/MEANIE> App-Message-Id: <2028020119081995/A02131/MEANIE/119898421300> To: dave@wh.bayer.com, chemistry@www.ccl.net Subject: References to Aaquist and Mg2++ Sensitivity: Company-Confidential Dear David and all netters, Just a brief clarification; To scan scandinavian references on CAS may be rather "buggy". In scandinavia we have non-ascii charachters like a, and o with one or two dots above. They do not fit into the CAS browsing system, but may be spelled on CAS as: One dot over "a": a or aa; As in "J. Aqvist" or "J. Aaqvist" Two dots over "a": a or ae; As in "C. Branden" or "C. Braenden" Two dots over "o": o or oe; As in "H. Jornvall" or "H. Joernvall" Martin Norin Pharmacia Stockholm From jochen+@pitt.edu Fri Aug 18 20:34:03 1995 Received: from post-ofc02.srv.cis.pitt.edu for jochen+@pitt.edu by www.ccl.net (8.6.10/950810.1506) id UAA04301; Fri, 18 Aug 1995 20:32:41 -0400 Received: from unixs1.cis.pitt.edu (jochen@unixs1.cis.pitt.edu [136.142.185.20]) by post-ofc02.srv.cis.pitt.edu with SMTP (8.6.10/cispo-2.0) ID ; Fri, 18 Aug 1995 20:30:25 -0400 Date: Fri, 18 Aug 1995 20:30:25 -0400 (EDT) From: Jochen Kuepper Subject: Re: CCL:References to Aaquist and Mg2++ To: NOYM cc: dave@wh.bayer.com, chemistry@www.ccl.net In-Reply-To: <2028020119081995/A02131/MEANIE> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII And not only Scandinavian words, but almost every language has additional characters to the 26 known in the English language. Is there a common standard for interpreting them back to 26 ? Jochen From hinsenk@ERE.UMontreal.CA Fri Aug 18 21:19:04 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/950810.1506) id VAA04477; Fri, 18 Aug 1995 21:13:09 -0400 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by condor.CC.UMontreal.CA with ESMTP id VAA15020 (8.6.11/IDA-1.6); Fri, 18 Aug 1995 21:11:43 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id VAA01796; Fri, 18 Aug 1995 21:11:42 -0400 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id VAA18121; Fri, 18 Aug 1995 21:11:41 -0400 Date: Fri, 18 Aug 1995 21:11:41 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199508190111.VAA18121@cyclone.ERE.UMontreal.CA> To: jochen+@pitt.edu CC: martin.norin@sto.pharmacia.se, dave@wh.bayer.com, chemistry@www.ccl.net In-reply-to: (message from Jochen Kuepper on Fri, 18 Aug 1995 20:30:25 -0400 (EDT)) Subject: Re: CCL:References to Aaquist and Mg2++ And not only Scandinavian words, but almost every language has additional characters to the 26 known in the English language. Is there a common standard for interpreting them back to 26 ? No. Most countries have developed their own conventions when the upcoming telex system made this necessary, but they are all different. Sometimes there is even more than one convention for one language. BTW, even English needs more than 26 characters if spelt properly; there ought to be a difference between the verb "resume" and the noun "resum'e", for example. But in English the number of affected words is small enough to be ignored. Of the languages traditionally written in the Latin alphabet, only Latin itself needs no additional characters. And some that adopted the Latin script relatively recently (like Bahasa Indonesia, if I am not mistaken) are also content with the "standard" characters. Now, if anyone can find a relation back to chemistry... ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) -------------------------------------------------------------------------------