From arne@mango.mef.ki.se Tue Apr 13 09:30:59 1993 Date: Tue, 13 Apr 93 09:30:59 GMT From: arne@mango.mef.ki.se (Arne Elofsson) Message-Id: <9304130930.AA15894@mango.mef.ki.se> To: CHEMISTRY@ccl.net Subject: -visualizations on IBM/RS-6000. Dear Netters. Following the recent discussion about the possibilities to use x-windows based "free" molecular graphics packages I would like to make a comment: The only program we found that worked on an RS/6000 is squid by Mike oldfield (oldfield@yorvic.york.ac.uk) It is not very fancy for graphical presentations but it will atleast show a structure for a quick look. It also uses the GL packages if you work on a 3D-console. Besides the graphical interface it has the possibilities to analyse a structure or a trajectory. arne Elofsson PS. Please keep me posted if anyone port something fancier to the rs/6k From h8714031@hkuxa.hku.hk Tue Apr 13 05:54:26 1993 From: h8714031@hkuxa.hku.hk (Mok Kam Wah) Message-Id: <9304130935.AA17065@hkuxb.hku.hk> Subject: Question on Dynamic Electron Correlation. To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 13 Apr 93 17:35:25 WST Dear Sir, I am interesting in MCSCF calculation as most text mentioned that MCSCF is good in treating near degeneracy effect but still cannot deal with the dynamical correlation effect. I would like to know what is dynamical correlation effect? What is the physical meaning? Any suggested reading? Thanks for your kindness! -- K.W.Mok E-Mail: h8714031@hkuxa.hku.hk Dept. of Chem., University of Hong Kong. From EDWARDSP@vax.edinboro.edu Sat Apr 13 02:48:56 1993 Date: 13 Apr 1993 07:48:56 -0500 (EST) From: EDWARDSP@vax.edinboro.edu Subject: Xalpha To: chemistry@ccl.net Message-Id: <01GWYE4DMK7M9AO6KR@vax.edinboro.edu> There was a request a week or two ago for information on sources of Xalpha programs. This morning I received the following information from Prof. Bert te Velde. So far, this is the only lead I have received. Paul Edwards edwardsp@vax.edinboro.edu Edinboro University of PA --------------------------------------------------------- From: IN%"tevelde@chem.vu.nl" 13-APR-1993 07:15:07.43 To: IN%"edwardsp@vax.edinboro.edu" CC: Subj: Xalpha dear Paul Edwards, via the chemical requests I learned about your interest in an Xalpha program. Our density functional program ADF (Amsterdam Density Functional) has the X-alpha parametrization as one of the density functional options. ADF is commercially licensed. For academic institutions we ask a one-time fee of 1500 Dutch Guilders (approx. US$ 850) and (optionally) 500 Dutch Guilders per year for regular updates. If you are interested in a license I can send you an application form. regards, Bert te Velde Department of Theoretical Chemistry Vrije Universiteit De Boelelaan 1083 1081 HV AMSTERDAM The Netherlands tel: (+31) - (0)20 - 548 2978 fax: (+31) - (0)20 - 646 1479 e-mail: tevelde@chem.VU.NL From Leif.Laaksonen@csc.fi Tue Apr 13 18:15:38 1993 Date: Tue, 13 Apr 1993 15:15:38 +0300 Message-Id: <199304131215.AA23101@csc.fi> To: chemistry@ccl.net From: Leif.Laaksonen@csc.fi Subject: Programming molecular graphics Hi, I don't know how many of you reading this list do any graphics programming, if you don't you can trash this mail already now. As we all know a majority of the molecular graphics packages available are made for Silicon Graphics workstations using the GL library. We can also read from messages here that there is a demand for device independent molecular modelling programs based on X-windows. I'm rewriting now my graphics package to use OSF/Motif for the widgets but I'm not quite sure what I should use for the graphics. Now I would like to ask your opinion about the different available application programmer's interfaces (API). (a) What library would you use for creating the widgets? (b) Would you go for PEX or OpenGL or is there anything else? (c) Do you know about any good application builders to create the widgets? I don't wish to turn this into a war between different religions like the known Fortran against C battle but I just would like to stimulate some discussion about this subject. Peace, -Leif Laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Telefax: 358 0 4572302 FIN-02101 Espoo | Voice Mail: 358 486257407 FINLAND | Mail: Leif.Laaksonen@csc.fi One of these days I'm going to sit down and write a long letter To all the good friends I've known One of these days by Neil Young ------------------------------------------------------------------- From DSMITH@uoft02.utoledo.edu Tue Apr 13 05:07:59 1993 Date: Tue, 13 Apr 1993 10:07:59 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: stereo viewing in molecular modeling To: chemistry@ccl.net, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Message-Id: <01GWYIOSODWI003Q7I@UOFT02.UTOLEDO.EDU> I have a general question for anyone out there who wishing to open a dialog about stereo viewing for molecular modeling. Please send responses directly to me and I will summarize for the net. Most graphical user interfaces have provided a limited version of stereo viewing capability for years. This typically involves presenting a right and left eye view on screen, where one view is rotated slightly with respect to the first. Three dimensional viewing required the user to cross his/her eyes and focus the two images one on top of the other. With high resolution monitors using refresh rates of 120 Hz, stereoscopic images are produced by rendering alternating left and right images on the screen (i.e. each appears 60 times per second) while the user wears special glasses. The technology has advanced to the point where it is no longer uncomfortable to wear or use the glasses. The image seen now has true perspective and dimension in the z direction (into the screen). Is this type of three-dimensional viewing of use in molecular modeling, or is the current use of shading, etc. to generate flat 2D representations of 3D objects sufficient? Note that even with the stereo glasses, as one moves relative to the screen, i.e. changes the direction of viewing from straight on to side on, one still never sees any additional portions of the image which were previously hidden. That requires moving the object on the screen. In addition to opinions, I would like to hear success stories where the use of 3D viewing has enhanced the chemistry or helped to solve a problem which was insoluble without it or would have taken a longer time or would have resulted in a lower quality answer. Finally, thoughts on virtual reality for molecular modeling are solicited as well. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From mail Tue Apr 13 09:49:28 1993 From: hyper!slee (Thomas Slee) Message-Id: <9304131349.AA05659@hyper.hyper.com> Subject: HyperChem Release 3 for Windows Commercial Announcement To: chemistry@ccl.net Date: Tue, 13 Apr 1993 09:49:24 -0400 Hypercube has completed HyperChem(TM) Release 3 for Windows(TM). HyperChem is licensed to Autodesk(R), Inc., who have announced that it will be available this month. Major new features of Release 3 include: easy control over stereochemistry, IR and UV spectra (and normal mode display) >from semi-empirical methods, additional file and clipboard formats, ribbons display of peptides and proteins, handling of up to twelve bonded neighbours, improved scripting and Windows DDE for customization and extension. Improvements to the semi-empirical quantum mechanics methods include a several-fold speed increase, INDO/1 and INDO/S methods for transition metals, computation of part of a system enabled for all methods, user-specified restraining forces to constrain geometries, and an interactive energy-level diagram for selection and analysis of molecular orbitals. More details are given in the file hyper.note in the OSC archives, ("send hyper.note from chemistry" message to OSCPOST@ccl.net). Autodesk, Inc. should be contacted for information about pricing and availability. For more information about Hypercube's services, including custom software and scientific support contracts for HyperChem, contact your Authorized HyperChem Dealer. Hypercube can be reached by phone at 519-725-4040, fax at 519-725-5193, and on Internet at info@hyper.com. Tom Slee From tevelde@chem.vu.nl Tue Apr 13 11:54:27 1993 Date: Tue, 13 Apr 93 17:22:07 MET DST Message-Id: <9304131522.AA10140@gallium.chem.vu.nl> To: CHEMISTRY@ccl.net From: tevelde@chem.vu.nl (Bert te Velde) Subject: Density Functional Program ADF (Amsterdam Density Functional) is a FORTRAN program for density functional calculations on molecules. It is the successor of the program known as AMOL or HFS. ADF is commercially licensed to industry and academia. For academic institutions the license fee is (for 1993) 1500 Dutch Guilders (approximately 850 US$). More information and application forms for a license can be obtained from: Bert te Velde Department of Theoretical Chemistry Vrije Universiteit De Boelelaan 1083 1081 HV AMSTERDAM The Netherlands tel: (+31) - (0)20 - 548 2978 fax: (+31) - (0)20 - 646 1479 e-mail: tevelde@chem.VU.NL From carolina@ce.ifisicam.unam.mx Mon Apr 12 16:12:02 1993 Message-Id: <199304131556.AA29820@oscsunb.ccl.net> From: Carolina Subject: MEP derived charges To: CHEMISTRY@ccl.net (SEND_NEWS) Date: Mon, 12 Apr 93 21:12:02 CDT Dear Netters: I am looking for information as where (if there is any) I could get from public sources a program to calculate atomic charges derived from electrostatic potential. Any help will be appreciated. Cheers. -- ___________________________________________________________________ CAROLINA GODOY-ALCANTAR Facultad de Ciencias Universidad del Edo. de Morelos Chamilpa, Morelos. email: carolina@ifisicam.unam.mx From ramon@ce.ifisicam.unam.mx Mon Apr 12 16:08:35 1993 Message-Id: <199304131556.AA29842@oscsunb.ccl.net> From: Ramon Garduno Subject: Looking for MM2/MM3 software. To: CHEMISTRY@ccl.net (SEND_NEWS) Date: Mon, 12 Apr 93 21:08:35 CDT Dear Netters: I am in the process of publishing a paper, but a reviewer suggested to perform some calculations on the molecules I report with either MM2(87) or better yet MM3. However, I do not have access to any of them. Does any body knows where I can put my hands unto these programs? If they are from public sources, it will be appreciated. Thanks in advance. -- _______________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF ___________________________________________ From ramon@ce.ifisicam.unam.mx Mon Apr 12 16:03:26 1993 Message-Id: <199304131556.AA29832@oscsunb.ccl.net> From: Ramon Garduno Subject: Looking for Prof. Harold Scheraga. To: CHEMISTRY@ccl.net (SEND_NEWS) Date: Mon, 12 Apr 93 21:03:26 CDT Dear Netters: I have been trying for the last two weeks to find either FAX or email address of Professor Harold Scheraga at Cornell University by gopher services with no luck. Does anybody have this information that want to share?. The main reason is to get ECEPP/3 from his group. I could send a letter to him, but you know that regular mail is not reliable. Sorry for the noise. -- _______________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA, UNAM || bitnet: rgard@unamvm1 Lab. de Cuernavaca || email: ramon@ifisicam.unam.mx Apdo. Postal 139-B || 62191 Cuernavaca, Morelos || FAX: (73)173077 MEXICO || (73)111603 ______________________________ EOF ___________________________________________