From owner-chemistry@ccl.net Fri Aug 16 00:17:50 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id XAA12958; Thu, 15 Aug 1996 23:19:09 -0400 (EDT) Received: from seagoon.newcastle.edu.au for tony@schroeder.newcastle.edu.au by bedrock.ccl.net (8.7.5/950822.1) id XAA00685; Thu, 15 Aug 1996 23:19:04 -0400 (EDT) Received: from pigpen.newcastle.edu.au (pigpen.newcastle.edu.au [134.148.36.9]) by seagoon.newcastle.edu.au (8.7.5/8.7.3) with SMTP id NAA15874 for ; Fri, 16 Aug 1996 13:18:55 +1000 (EST) Sender: tony@seagoon.newcastle.edu.au Message-ID: <3213E892.41C6@schroeder.newcastle.edu.au> Date: Fri, 16 Aug 1996 13:18:42 +1000 From: Tony Dyson Organization: University of Newcastle X-Mailer: Mozilla 3.0b7 (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: Computational Chemistry List Subject: CCL: ChemExhibit cut & paste Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are using the ChemExhibit package by Molecular Arts to prepare figures for publication, depicting 3-D structures obtained from our theoretical calculations. In some ways we have been very happy with the package, because it provides a fairly simple yet powerful set of manipulation tools for dealing with 3-D structures. There has been one aspect of the system though that has caused us an immense amount of frustration. This involves cutting and pasting 3-D figures from ChemExhibit into other Windows applications. Under Windows for Workgroups 3.11, this produces very poor printed results. For example, if I "select all" in Exhibit and copy and paste into Paint, then immediately print, all colour information from the atoms is lost and the output contains solid black circles instead of shaded atoms. Also the text becomes very chunky and jagged. Meanwhile printed output directly from Exhibit is very good. Pasting into MS-Word 6 is marginally better but still the quality of the printed figures is much degraded with respect to direct output from Exhibit. I would be interested to know whether other users of this package have experienced similar difficulties, and even more interested to hear about any workarounds or fixes that may exist. Tony Dyson -- ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +61 49 21 5565 University of Newcastle fax: +61 49 21 6907 Callaghan, Australia, 2308 ================================================================ From gford@post.smu.edu Fri Aug 16 13:18:00 1996 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.7.5/950822.1) id NAA16237; Fri, 16 Aug 1996 13:08:53 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Fri, 16 Aug 96 12:08 CDT Message-Id: Date: Fri, 16 Aug 96 12:08 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: Stereo images using colored glasses Can somebody tell me if any modeling packages other, than Spartan, allow the user to visualize stereo images using a pair of red/blue glasses? George P. Ford ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================ From jin@proteus.co.uk Fri Aug 16 14:17:58 1996 Received: from sys4.cambridge.uk.psi.net for jin@proteus.co.uk by www.ccl.net (8.7.5/950822.1) id NAA16280; Fri, 16 Aug 1996 13:18:09 -0400 (EDT) Received: from proteus.co.uk by sys4.cambridge.uk.psi.net (8.7.5/SMI-5.5-UKPSINet) id SAA29461; Fri, 16 Aug 1996 18:11:03 +0100 (BST) From: "Jin Li" Message-Id: <9608161710.ZM5057@Einstein> Date: Fri, 16 Aug 1996 17:10:47 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Computational Chemist Position Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Computational Chemist An opportunity has arisen for a computational chemist to join the Computational Chemistry Section at Proteus Molecular Design Ltd. Proteus is a drug discovery research based company with its core technology in computer-aided molecular design. Proteus is based in Macclesfield, Cheshire, UK. For this particular position, applications are invited from individuals who have a PhD degree in computational chemistry or related areas. The successful applicant will need to have demonstrable expertise and experience in CAMD software development and applications. Specifically, the applicant will nedd to have a good working knowledge of chemistry, an ability to program in C and/or FORTRAN in a UNIX environment, and a strong background in molecular modelling and drug design. Working experience in a pharmaceutical company's molecular modelling group will be an advantage. The successful applicant will join a team of dedicated computational scientists working on the development of CAMD technologies (e.g., structure-based design of combinatorial libraries, and receptor-ligand docking, etc), and their application in drug design. Proteus offers an attractive remuneration and benefits package which is appropriate to the candidate's ability and experience. If you have the appropriate background and experience, please apply with full CV to: Human Resources Administrator, Proteus Molecular Design Ltd., Proteus House, Lyme Green Business Park, Macclesfield, Cheshire SK11 0JL, UK. Tel,: (UK) 1625 500555; Fax: (UK) 1625 500666. Jin Li, PhD Head of Computational Chemistry From raman@bioc01.uthscsa.edu Fri Aug 16 16:18:01 1996 Received: from elzip.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.7.5/950822.1) id PAA16991; Fri, 16 Aug 1996 15:52:05 -0400 (EDT) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01I8CIPUKM4O006RR8@uthscsa.edu> for chemistry@www.ccl.net; Fri, 16 Aug 1996 14:51:48 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA12878; Fri, 16 Aug 1996 14:50:39 -0500 (CDT) Date: Fri, 16 Aug 1996 14:50:35 -0500 (CDT) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: coordinates... To: chemistry@www.ccl.net Message-id: <9608161950.AA12878@bioc01.uthscsa.edu> X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Dear CCL readers: Is anyone aware of the existence of coordinates for the following compounds in the Cambridge Database? L-Histidine, Cimetidine, imidazole, 1-methyl-imidazole and histamine. Any input would be appreciated. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 614-0839 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From FAU@ps1515.chemie.uni-marburg.de Fri Aug 16 17:18:00 1996 Received: from Mailer.Uni-Marburg.DE for FAU@ps1515.chemie.uni-marburg.de by www.ccl.net (8.7.5/950822.1) id QAA17341; Fri, 16 Aug 1996 16:31:46 -0400 (EDT) Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 3.2/UCB 5.64/20.07.94) id AA37297; Fri, 16 Aug 1996 22:31:42 +0200 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 16 Aug 96 22:34:03 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 16 Aug 96 22:33:45 GMT+2 From: "Stefan Fau" To: chemistry@www.ccl.net Date: Fri, 16 Aug 1996 22:33:38 MDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: G: Wrong Freq - insufficient convergence Return-Receipt-To: "Stefan Fau" Priority: normal X-Mailer: Pegasus Mail for Windows (v2.01) Message-Id: <16E33A43EBD@ps1515.chemie.uni-marburg.de> Hi, here are my thoughts concerning the difference between frequencies and Low-frequencies. If I tell something wrong, feel free to correct me! (a), we encounter the same phenomenon, if we calculate molecules with very flat PES's. An extreme example is H3C-Be-CH3 (D3d) at the MP2/6-32G(d) level. When the structure is converged to about half of the standard limits, the biggest of the six "Zero"-frequencies is 52 cm-1 and the next Low-frequency is 55 cm-1. I do not recall the corresponding value in the complete list of frequencies, but it was different. However, after reoptimization of the molecule with the very-tight limits, we got very good agreement between frequencies and Low-frequencies. The first 6 Low-frequencies were between -1.36 and -0.00 and the next three were 18.11, 201.01, 201.01. The corresponding frequencies match perfectly. (b), we assume that the frequencies and Low-frequencies are calculated with different algorithms, which include different approximations and should both be correct with a perfectly converged structure. But, as nothing is perfect, in practice the results differ a little bit. (c), the softer the PES around your structure is, the greater are the differences of the two algorithms. Therefore we consider it a problem of the convergence criteria. We always got good agreement between frequencies and Low-frequencies, when we reoptimized the structure (e.g. opt=(readfc,tight)). As the standard convergence criteria are made for standard molecules, problems can arise with very soft molecules. Therefore I use the agreement between frequencies and Low frequencies as an additional criterion for convergence. I arbitrarily chose a maximum difference of 0.01 cm-1 between corresponding freqs and Low-freqs as sufficient and also look, if the ratio of the biggest "Zero"-freq and the first "real" freq exceeds (-)25. Maybe somebody can comment on this? Stefan Stefan Fau, fau@ps1515.chemie.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. D-35032 Marburg