From lindsay@qtp.ufl.edu Fri Jan 5 11:53 EST 1996 Received: from qtp.ufl.edu for lindsay@qtp.ufl.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA19521; Fri, 5 Jan 1996 11:53:54 -0500 (EST) Received: from admin1.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/4.11) id LAA08617; Fri, 5 Jan 1996 11:53:52 -0500 Received: by admin1.qtp.ufl.edu (SMI-8.6/4.11) id LAA24966; Fri, 5 Jan 1996 11:53:46 -0500 From: "Denise Lindsay" Date: Fri, 5 Jan 1996 11:53:46 -0500 Message-Id: <199601051653.LAA24966@admin1.qtp.ufl.edu> Subject: Quantum Chemistry Workshop (ACESII) in June To: chemistry@www.ccl.net "Rod Bartlett and the authors of ACES II are tentatively planning a fourth ACES II, and ab initio quantum chemistry workshop, to be held in June, at the University of Florida, Gainesville, FL. Through a cooperative arrangement with IBM, the workshop will be conducted on the new IBM 39H workstations. The tuition for the three and one-half day course is $500. Housing will be available at the Reitz Union hotel on campus at $30-40 a day. The intent of this message is to inquire whether there is sufficient interest to finalize the dates of the proposed workshop. Attendance is limited to 20 people. If interested, please contact aces2@qtp.ufl.edu." aces2@qtp.ufl.edu From VARNAI@ch.bme.hu Tue Dec 12 13:26:10 1995 Received: from ns.bme.hu for VARNAI@ch.bme.hu by www.ccl.net (8.6.10/950822.1) id NAA17376; Tue, 12 Dec 1995 13:25:45 -0500 Received: from ch.bme.hu (ch.bme.hu [152.66.64.1]) by ns.bme.hu (8.6.12/8.6.12) with SMTP id TAA15508 for ; Tue, 12 Dec 1995 19:25:39 +0100 Received: from CH/TEMPQ by ch.bme.hu (Mercury 1.12); Tue, 12 Dec 95 19:24:41 +1100 Received: from TEMPQ by CH (Mercury 1.12); Tue, 12 Dec 95 19:24:24 +1100 From: "Varnai Peter" To: chemistry@www.ccl.net Date: Tue, 12 Dec 1995 19:24:15 GMT+100 Subject: summary of CAS questions Message-ID: <69FA130961@ch.bme.hu> Dear CClers, A little late, but I send You the summary. My thanks to those (Frank Jensen, Mathias Bock, Doug Fox) who sent me their comments. Yes, it is not an easy question how to select the active space of an e.g. transition state. In my view there are some methods, but none of them is always applicable: 1, visualization (what is the chemical problem) 2, orbitals weights in CI calculations 3, occupancy number of the orbitals. Important to check the orbitals of the structures around your initial structure to create a consistent active space! Be careful, sometimes occ. number or weights tell you chemically not important orbitals eg pi-orbitals in a sigmatropic shift (hard to answer whether it is a mistake to include those beyond the essential orbitals; whether CAS is ONLY for the non-dynamic part of the correlation energy etc). Gaussian 94 is indeed have a new routine which seems to converge better, but allow you to create nonsense as well. But, don't lose the chk file, hard to recover it! In case somebody has new ideas, those are always welcome! Here follows the original letter and the answers. Again, thank You! Peter Varnai ??????????????????????????????????????????????????????????????? I would need Your help to understand the practical tricks in CASSCF calculations. 1, One needs to define an active space. -At this point quantum chemists start to think as the conventional organic chemist,in localized orbitals. Here those orbitals needed -in view of a chemist- that are involved in a eg. reaction (forming/breaking orbitals). -A more exact answer would be that those orbitals needed which are important in "excitation" to give configurations that contribute to the total energy significantly. So: -according to the first approach one would visualize the MOs. Here he/she would realize that in MO theory the orbitals are spread all over the molecule, so the needed eg C-C bond will appear in at least 3 MOs. Which one should be used then? Let's use all (unfortunately, the valence MOs usually can't be all involved in the active space)? Let's localize the MOs with standard methods? Pick one random and what happens (the one is better than the other if using it the SCF energy is lower)? -according to the more "mathematical" approach let's calculate a CISD wavefunction [in the absence of the full CI :(] and involve the orbitals which are involved in large coefficient (say 0.03<) determinants? And what if the HF reference function was not a good approximation and some important determinants are missed? -If I am right CAS should be used as the correction to the non- dynamic electron correlation (through the the right geometry and wavefunction). What happens then when CISD tells you that an orbital energetically important though not needed in view of the reaction, description of the radical etc. it would be some parts of the dynamic correlation effect then?! 2, CASSCF in Gaussian 92 for me (and I guess for several others) stopped with the error message: rotation larger than 45 degree... If I understand well either a smaller step in wavefunction optimization would have been desirable or the active space was not well chosen and a non-selected orbital was crucial in the active space. Yet, I haven't got error message like this with the G94 routine, only warnings that large rotations are scaled and something like: I J= 12 26. I don't really understand the meaning of these numbers (i,if these are MO numberings, I have to say that eg MO- 12 was not selected to be in the active space, ii, in MOLCAS for example the user can define only the number and symmetry of the active orbitals, the exact MO not, how will then the routine pick the right orbital? iii, is it allowed to change orbitals of the active space during SCF). 3, In case one loses the chk file and would like to keep it for further use, is the following way is correct to create the same chk file? 1, Calculate the HF-MOs at the starting geometry once again and picking the same MOs 2, converging the CAS wavefunction as it was done in the previous calculation and 3, reading in the wavefunction (to have the same active space) and having the converged CAS-geometry (not to redo the whole previous calculation). If it is correct can anyone tell me why I did not reproduce the same stationary point, but locating an other one (higher in energy). (As I know this method is used when one tries to find the right active space in a supermolecule by isolating it to fragments). If You had the patience and read my letter through, and You can help me in using CAS smoothly: THANK YOU! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Varnai, one of the 'modern' ways of selecting the active MOs in a CASSCF is from the natural orbital occupation numbers, i.e. first do a MP2 or CISD and diagonalize the density matrix to giv ethe natural orbitals. Then select the orbitals which have occupation number 'significantly' different from 0 or 2. How far away depends on your problem (and hardware!) but typically orbitals with occ. >0.05 and < 1.95 must be included, and >0.03 and < 1.97 is desireable. Since CASSCF wave functions often are used for many different geometries (like a reaction), you need to do this at several points, and select a 'consistent' space, i.e. the smallest which include all the 'important' orbitals at each geometry. In some cases it will be difficult to make a consistent choice. So, as you can se from the 'quotes', CASSCF orbital selection is not easy. Frank !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Hallo Peter, your CASSCF questions were quite familar to me, unfortunetaly I am not able to answer them totally, maybe the specific G9x answers will come from help@gaussian.com if you havenot already done so. First of all, I should prefer to use several CI-methods to look for the most important configurations to be included. You can decide whether static correlation is included at a minimum of cost. In G92 CASSCF/6-31G gave nice results, even for open-shell molecules. The choice of orbitals was crucial. Sometimes I used sophisticated pre-runs to get starting orbitals. But this is no garanty to converge even from a converged ground state to reach convergence for an excited state. G94 will not care as much as G92, so don't get slippy ! Running small basis sets, gives an easy initial choice, but it happened not to give SCF-convergence, until another starting geometry was given. Good starting geometries were given by UHF/3-21G or RMP2/6-31G*. The open-shell UHF/ROHF gives you another riddle, as the UHF-functions don#t give reliable wave functions. The use of CISD seems necessary to annihilate spin contamination. Also try an RHF-guess first by changing charge and multiplicity. I hope a summary of answer will go to net. If not, I would appreciate a copy. Thanks . Mathias Brock !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Peter, The choice of active space is the most challenging part of getting a CASSCF right. WE have changed the code with G94 to make failures like "rotation larger than 45 degrees" go away but with an intellectual cost. The meaning of this error, as I think we have discussed, is to switch a pair of orbitals changing the active space. To avoid this G94 damps this rotation to keep it from switching and force a solution within the chosen active space. The reason behind not adapting MolCAS's behavior is that you most often want to study a particular state or reaction with a CAS wavefunction. This may well not be the lowest energy solution and if the active space is allowed to change you may well end up with the wrong state or with the wrong active space for the reaction of interest. For example if you are looking at formaldehyde loosing H2 the lowest energy solution is to include the pi orbitals but these play no part in proper dissociation to H2 + CO. The penalty for not allowing the switch is a poor initial guess may end up not describing the orbital you wanted or an ill chosen guess can include orbitals which don't interact with the orbitals that define/control the reaction/state of interest. Thus for G94 what you want to do is pick your active space as well as possible and then examine the result of a single point calculation. Make sure that there are not orbitals with double or zero occupancy. Use #P to get this printed out. If there are then the eigenvector for that state, key back to the list of configurations printed earlier, can let you see which orbitals are likely candidates either to be removed or switched. The goal is to make the solution match your state of interest not simply a lowest energy solution. Restarting can be a bit of a problem. First, you may well have moved to a part of the surface where the RHF solution is a lousy representation. Using STABLE=OPT to make sure that you get the best single determinant is worthwhile. Your plan of starting from the initial orbitals and then leaping to the final structure seems reasonable as well. There are changes to the orbitals as the optimization progresses. These changes may make the difference between the "excited" state you found and the state you optimized to. Is your case small enough that you can try the CASSCF(QC) option, requires writting AO integrals to disk, this may well be able to get past the problem. Doug Fox help@gaussian.com !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! From LUTTMANN@RP.FR Wed Dec 27 03:14:01 1995 Received: from xr1.atlas.fr for Claude.C.LUTTMANN@VITRY.RPR/RD/CRVA/CHIMIE.RP-RORER.rp.fr by www.ccl.net (8.6.10/950822.1) id DAA02140; Wed, 27 Dec 1995 03:13:58 -0500 From: LUTTMANN@RP.FR Date: Wed, 27 Dec 1995 09:49:32 +0100 X400-Originator: Claude.C.LUTTMANN@VITRY.RPR/RD/CRVA/CHIMIE.RP-RORER.rp.fr X400-Recipients: chemistry-request@www.ccl.net X400-MTS-Identifier: [/PRMD=RP/ADMD=ATLAS/C=FR/;SSWA 951227084928544261] X400-Content-Type: P2-1984 (2) Content-Identifier: RE : CCL:Synthet Message-ID: <"SSWA 951227084928544261@RP.FR> To: chemistry@www.ccl.net> Subject: RE : CCL:Synthetic Accessibility Dear Chris, Following your message of 30-NOV-1995 on the CCL server I answered you that I had some reference taht could be of interest to you and other CCLer's. In fact I have references corresponding to Reaction database classifications, Reaction database searching systems, retrosynthetic pathway analysis and computer assisted organic synthesis. Hereafter are some references for these specific topics but I do not know about a program that is specifically dedicated to the problem of chemical feasability. 1.- Retrosynthetic pathway analysis and computer assisted organic synthesis : I think that it is not worth to recall the LHASA program (Corey) as well as the CASEA program that is under development at the University of Leeds by Pr. Peter Johnson's group. Some references : "COmpeting concepts in CAOS", A. Dengler et coll., Receuil des travaux chimiques des Pays-Bas,111,262-269, 1992. "A collection of computer methods for synthesis design and reaction prediction", J. Gasteiger et coll., Receuil des travaux chimiques des Pays-Bas,111,270-290, 1992 "Computer tools for reaction retrieval and synthesis planning in organic chemistry", Receuil des travaux chimiques des Pays-Bas, 111/6, june 1992, 239-246. "SOPHIA, a knowledge base-guided reaction prediction system. Utilization of knowledge base derived from reaction database", J. Chem, Inf. Comput. 1995, 35, 34-44. "CONAN(CONnectivity ANalysis) : A simple approach in the field of computer-aided organic synthesis. Example of the taxane framework." R. Barone et coll., J. Chem, Inf. Comput. 1995,35,467-471. "Generalization and representation of synthesis pathways in the COSYMA system" G. Kaufmann et coll. Receuil des travaux chimiques des Pays-Bas,111/6,June 1992, 317-322. "Computer-executed synthesis planning, a progress report" Receuil des travaux chimiques des Pays-Bas,111/6,June 1992,291-296. "Context description in Synthesis Planning",J. Chem, Inf. Comput. 1994,34,117-119. "A preliminary appraisal of selected problems in computer-assisted organic synthesis",Receuil des travaux chimiques des Pays-Bas,111/6,June 1992,255-261. 2.- Reaction database searching systems : Some netters spoke also about SYNLIB. Hereafter a reference: "SYNTHESIS LIBRARY, an expert systgem for chemical-reaction knowledge-base management", D.F. Chodosh et coll., Receuil des travaux chimiques des Pays-Bas, 111/6, June 1992, 247-254. "Similarity concepts for the planning of organic reaction and syntheses" J. Gasteiger et coll., J. Chem, Inf. Comput. 1992,32,700-712. 3.- Reaction database classifications : MDL have developped classification methods for reaction databases in collaboration with some germanic information system company (I do not remember the name). "HORACE: An automatic system for the hierarchical classification of chemical reactions" Gasteiger et coll., J. Chem, Inf. Comput. 1994, 34,74-90. Clearly there are programs or procedures to be developped for adressing chemical feasability and one of the solution may the exploitation of reaction databases and the other being CAOS. A combination of the two may be even better. Hope this helps Dr. Claude LUTTMANN * Rhone-Poulenc RORER - CRVA * Tel: +France-1-45-73-78-30 B.P. 14 13, quai Jules Guesde * Fax: +France-1-45-73-80-14 94403 Vitry-sur-Seine Cedex France * Email: LUTTMANN@RP.FR From owner-chemistry@ccl.net Tue Jan 2 12:15:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA03155; Tue, 2 Jan 1996 12:15:02 -0500 Received: from xray0.chem.arizona.edu for BWESTCOTT@xray0.chem.arizona.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA01056; Tue, 2 Jan 1996 12:15:00 -0500 (EST) Date: Tue, 2 Jan 1996 10:12:30 MST From: BWESTCOTT@XRAY0.CHEM.ARIZONA.EDU (The Big Guy) Message-Id: <960102101230.202044a7@XRAY0.CHEM.ARIZONA.EDU> Subject: Lattice programs? To: chemistry@ccl.net Hi everyone, I was wondering if anyone could tell me if there is a good packing program in which one can introduce an impurity and then minimize the geometry of the system. I am currently working on single crystal epr studies and we are doping the paramagnetic complexes into diamagnetic host lattices to elimiunate interactions between neighboring paramagnets. Here I have access to Cerius, but I am not convinced that it can do what I want. Simply, I want to import the lattice parameters from the crystal structure, then remove one unit and replace it with the paramagnetic complex. Than I want to minimze the structure to see how the paramagnetic complex's geometry changes when doped into the diamagnteic host lattice. Any help would be greatly appreciated. Barry Westcott University of Arizona bwestcott@xray0.chem.arizona.edu From 100411.2306@compuserve.com Wed Jan 3 04:12:57 1996 Received: from dub-img-4.compuserve.com for 100411.2306@compuserve.com by www.ccl.net (8.6.10/950822.1) id EAA10059; Wed, 3 Jan 1996 04:12:55 -0500 Received: by dub-img-4.compuserve.com (8.6.10/5.950515) id EAA04302; Wed, 3 Jan 1996 04:12:25 -0500 Date: 03 Jan 96 04:10:36 EST From: Heinz Hofmann <100411.2306@compuserve.com> To: CCL Subject: Temperature dependent data of organic compounds Message-ID: <960103091036_100411.2306_BHG49-1@CompuServe.COM> Dear Netters, I am particulary interested in the temperature dependence of the density, viscosity, heat capacity and vapor pressure of organic compounds. Can anybody point me to a book, electronic database, CD ROM, www site etc. where I can find the information in a compressed form ? Thanks for your help & best regards Heinz ******************************************** Dr. Heinz Hofmann Sandrangen 3 D-91257 Pegnitz-Buchau Germany Phone : +49-9241-91216 Fax : +49-9241-91217 Internet : 100411.2306@compuserve.com ******************************************** From owner-chemistry@ccl.net Wed Jan 3 14:20:50 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA16899; Wed, 3 Jan 1996 14:20:49 -0500 Received: from gardel.psc.edu for mmadrid@gardel.psc.edu by bedrock.ccl.net (8.7.1/950822.1) id OAA12912; Wed, 3 Jan 1996 14:20:46 -0500 (EST) Received: by gardel.psc.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA07965; Wed, 3 Jan 96 14:20:07 -0500 From: "Marcela Madrid" Message-Id: <9601031419.ZM7963@gardel.psc.edu> Date: Wed, 3 Jan 1996 14:19:57 -0500 To: chemistry@ccl.net Subject: CCL: biomedical workshops at the PSC Biomedical Workshops typically consist of theoretical lectures taught by leaders in the respective scientific discipline, and extensive hands-on computer sessions. During the computer sessions, participants are able to work on the examples provided or on their own experimental data. Attendance is limited to 20 participants to allow one-on-one instruction and encourage scientific interactions and discussions. Application deadlines are six weeks prior to the workshop. Researchers nationwide are invited to apply. The following four workshops will be offered during 1996. For additional information on Biomedical Workshops, please refer to the online material at URL http://www.psc.edu/biomed/workshops.html Supercomputing Techniques for Biomedical Researchers; May 6-10, 1996. The purpose of this workshop is to introduce attendees to the concepts of supercomputing. The main goal is to provide researchers a firm basis from which to analyze their applications for implementation in a supercomputing environment. After a brief introduction to PSC's supercomputing environment, including the architectures of the CRAY C90 and T3E, various vector and massively parallel programming models, their differences and similarities, their strengths and weaknesses will be discussed. Message passing, performance monitoring, optimization techniques, and heterogeneous supercomputing will be introduced with emphasis on practical considerations. Specific real-world biomedical supercomputing applications will be presented to illustrate these concepts. Finally, a panel discussion will attempt to address researchers' individual application questions. Nucleic Acid and Protein Sequence Analysis; June 9-14, 1996. Emphasis will be on alignment of and pattern extraction from multiple sequences. Topics to be discussed include Comparing and aligning sequences Identifying informative patterns in a set of sequences Using extracted informative patterns to identify related sequences. Leaders are Dr. Gary Churchill, Cornell University, Dr. Hugh B. Nicholas, Jr., Pittsburgh Supercomputing Center and Dr. Michael Gribskov, San DIego Supercomputing Center. Methods and Applications of Molecular Mechanics and Dynamics to Molecules of Biological Interest; August 7-10, 1996. Instructors include Prof. Peter A. Kollman, UCSF, Dr. David Case, the Scripps Research Institute, Thomas Cheatham, UCSF, and Bill Ross, UCSF. General aspects of molecular mechanics and dynamics theory and software will be discussed. The program AMBER will be utilized extensively in demonstrations. Advanced Nucleic Acid and Protein Sequence Analysis; Dates TBA. Open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have appreciable experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for analyzing families and superfamilies of genes and proteins. From mjchoi@indigo2.kist.re.kr Thu Jan 4 21:08:37 1996 Received: from indigo2.kist.re.kr for mjchoi@indigo2.kist.re.kr by www.ccl.net (8.6.10/950822.1) id VAA02760; Thu, 4 Jan 1996 21:08:33 -0500 Received: by indigo2.kist.re.kr (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA29670; Thu, 5 Jan 95 11:22:03 -0800 Date: Thu, 5 Jan 95 11:22:03 -0800 From: mjchoi@indigo2.kist.re.kr (Mun-Jeong Choi) Message-Id: <9501051922.AA29670@indigo2.kist.re.kr> To: chemistry@www.ccl.net Subject: krypton (or xenon) clusters Dear netters, Does anyone know the reference(s) about global minimum geometries of krypton (or xenon) clusters? Thanks in advance. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Mun-Jeong Choi Doping Control Center Korea Institute of Science and Technology Tel : 02-958-5058 e-mail : mjchoi@indigo2.kist.re.kr mjchoi@kistmail.kist.re.kr @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ From owner-chemistry@ccl.net Fri Jan 5 15:54:40 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA18713; Fri, 5 Jan 1996 15:54:39 -0500 Received: from asrr for srheller@nalusda.gov by bedrock.ccl.net (8.7.1/950822.1) id PAA25315; Fri, 5 Jan 1996 15:54:28 -0500 (EST) Received: from golem1..arsusda.gov (GOLEM1.ARSUSDA.GOV) by asrr (5.x/SMI-SVR4) id AA14948; Fri, 5 Jan 1996 15:55:27 -0500 Message-Id: <9601052055.AA14948@asrr> Date: Fri, 05 Jan 96 16:50:27 -0800 From: Steve Heller To: chemistry@ccl.net Subject: ACS Book: http://pubs.acs.org/books/catalog/32237.htm New from ACS Books The Internet A Guide for Chemists Computer Applications in Chemistry Books Steven M. Bachrach, Editor Stephen R. Heller, Consulting Editor ISBN 0-8412-3223-7 (clothbound) LC 95-41967 Catalog No. 419-32237 350 pages. Cloth. (1996) $29.95 ISBN 0-8412-3224-5 (paper) LC 95-41967 Catalog No. 419-32237 350 pages. Cloth. (1996) $23.95 Excerpt The Internet. You can't read a newspaper or magazine that doesn't have about a dozen references to it. Everywhere you look, there is mention of something on the Internet. It seems that if you don't know what e-mail, Gopher, FTP, WAIS, and the World Wide Web are, you might as well be marooned on a desert island. If you're in that category, or even if you're already on the Internet, you need this book. In a stepwise and thorough manner, this book presents the basics of the Internet along with instructions on becoming an information provider on the Internet. It also gives useful information specific for chemists, such as Web addresses, electronic mailing lists, Gopher sites, and FTP sites. In 13 chapters, this well-organized, easy-to-use book contains information for novices and advanced users who want tips on chemistry-related aspects of the Internet. This book is an invaluable desk reference for chemists in all disciplines. -------------------------------------------------------------------- Contents Basic Information 1. History of the Internet Laurence R. Dusold 2. Electronic Mail Jan K. Labanowski, Charles F. Bender, and Alejandro Pisanty 3. The Berkeley Mail Program Jan K. Labanowski, Charles F. Bender, and Alejandro Pisanty 4. Electronic Lists Jan K. Labanowski, Charles F. Bender, and Alejandro Pisanty 5. Gopher Steven M. Bachrach 6. The World Wide Web Henry S. Rzepa 7. Designing an Internet-Accessible Database Frank A. Tinker 8. Electronic Conferencing Thomas C. O'Haver Specifically for Chemists 9. Electronic Lists for Chemists Jan K. Labanowski, Charles F. Bender, and Alejandro Pisanty 10. Managing the Computational Chemistry List Jan Labanowski, Charles F. Bender, and Alejandro Pisanty 11. Chemistry and Gopher Steven M. Bachrach 12. Chemistry and the World Wide Web Henry S. Rzepa 13. Chemical Industry and the Internet: An Explosion of Opportunity T. H. Pierce and T. J. Cozzolino -------------------------------------------------------------------- Books Catalog | ACS Books | ACS Departments and Services From modesto@luz.bq.ub.es Wed Jan 3 07:03:11 1996 Received: from bedrock.ccl.net for modesto@luz.bq.ub.es by www.ccl.net (8.6.10/950822.1) id HAA11418; Wed, 3 Jan 1996 07:03:10 -0500 Received: from luz.bq.ub.es for modesto@luz.bq.ub.es by bedrock.ccl.net (8.7.1/950822.1) id HAA08601; Wed, 3 Jan 1996 07:03:03 -0500 (EST) Received: by luz.bq.ub.es (940816.SGI.8.6.9/940406.SGI) for chemistry-request@ccl.net id MAA13981; Wed, 3 Jan 1996 12:45:20 -0800 Date: Wed, 3 Jan 1996 12:45:20 -0800 From: modesto@luz.bq.ub.es (modesto) Message-Id: <199601032045.MAA13981@luz.bq.ub.es> To: chemistry-request@ccl.net Subject: Br f-f parameters Dear all Are there any reference on reliable vW parameters for Br? Thanks --------------------------------------------------------------------- | Modesto Orozco | | | Prof. Biochemistry | | | Dep. Bioquimica | Phone: (343)402-1213 | | Universitat de Barcelona | Fax: (343)402-1219 | | Marti i Franques 1 | email: modesto@luz.bq.ub.es | | Barcelona, SPAIN 08028 | | --------------------------------------------------------------------- From shj@sbc2.kist.re.kr Wed Jan 3 23:22:05 1996 Received: from sbc2.kist.re.kr for shj@sbc2.kist.re.kr by www.ccl.net (8.6.10/950822.1) id XAA20597; Wed, 3 Jan 1996 23:17:29 -0500 Received: by sbc2.kist.re.kr (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id MAA22770; Thu, 4 Jan 1996 12:17:20 -0900 Date: Thu, 4 Jan 1996 12:17:20 -0900 From: shj@sbc2.kist.re.kr (sun-hee jung) Message-Id: <199601042117.MAA22770@sbc2.kist.re.kr> To: CHEMISTRY@www.ccl.net Subject: programs for genome assembly HI, Does anyone know programs available for genome assembly ? I'm interested in finding programs used for finding orders among many fragmented genomes to sequence and construct whole genome. Public domain (free) softwares are preferred, but also software that is sold for profit and their info are also welcomed. Many thanks !! ************************************************************************ Sun-Hee Jung KIST Structural Biology Center (L1150) Tel: (82-2) 958-5935 P.O. Box 131, CheongRyang Fax: (82-2) 958-5939 Seoul, 130-650, Korea Home: (82-2) 958-6425 e-mail:shj@sbc2.kist.re.kr (161.122.12.17) (English) e-mail:shjung@kistmail.kist.re.kr (161.122.12.3) (Korean) ************************************************************************ From frits@chemde4.leidenuniv.nl Thu Jan 4 04:51:58 1996 Received: from rulway.leidenuniv.nl for frits@chemde4.leidenuniv.nl by www.ccl.net (8.6.10/950822.1) id EAA22432; Thu, 4 Jan 1996 04:51:55 -0500 Received: from chemde4.LeidenUniv.nl by rulway.leidenuniv.nl with SMTP id AA27869 (5.67b/IDA-1.5 for <@RULWAY.LEIDENUNIV.NL:chemistry@www.ccl.net>); Thu, 4 Jan 1996 10:51:43 +0100 Received: by chemde4.leidenuniv.nl (920330.SGI/920502.SGI) for @RULWAY.LEIDENUNIV.NL:U54632%UICVM.BITNET@phem3.acs.ohio-state.edu id AA06212; Thu, 4 Jan 96 09:56:57 GMT Date: Thu, 4 Jan 96 09:56:57 GMT From: frits@chemde4.leidenuniv.nl (Frits Daalmans) Message-Id: <9601040956.AA06212@chemde4.leidenuniv.nl> To: U54632@UICVM.bitnet Subject: Re: CCL:4D-plots Cc: chemistry@www.ccl.net Hello, I know of a program that plots 4-D functions in a wireframe format, and rotates them around around 4 axes and projects them onto a 2-D screen. It works under X-windows. I don't know whether that is what you want, but it is the closest I ever got to finding a program to display 4-D data. Otherwise, you would have to look into using color as the fourth variable, thus giving it a special status with respect to the other three dimensions. The program is called 4va, was written by Matt Welsh, and is quite obscure. It is copyrighted, meaning you can't sell it and have to credit the original author(s). It can be found on ftp.funet.fi, /pub/Linux/util/X11/contrib, and also on the Linux mirror sites sunsite.doc.ic.ac.uk and ftp.cvut.cz. I do not know any mirror ftp site of ftp.funet.fi outside Europe at the moment.. archie couldn't find any.. Try tsx-11, or sunsite.unc.edu?? Hopefully this is of help, Frits Frits Daalmans OIO Conformational Analysis Gorlaeus Laboratoria Leiden, The Netherlands E-mail: frits@chemde4.leidenuniv.nl Tel: [+31] (0)71-5274505