From owner-hyperchem@hyper.com Tue Sep 5 19:00:47 1995 From: Massimo Trotta Subject: excel macros To: polowin@hyper.com Date: Tue, 5 Sep 1995 19:18:43 +0200 (MET DST) Cc: hyperchem@hyper.com Hallo everybody, I've been trying to retrieving the phipsia.xlm Excel macro via WWW connection. After a little struggling I was able to get the macro onto my Hard disk. Unfortunately the file (which is 41834 bytes large) cannot be opened by the Excel program. In other words I'm stuck with this unopenable file. Has anybody had a similar problem?: I have an Exel 4.0 version that runs in Italian. Any suggesion how to overcome this problem. Thanks Massimo Trotta csilmt12@area.cnr.ba.it Centro Studi Chimico-fisici sull'Interazione Luce Materia. ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 6 02:48:33 1995 Date: Wed, 6 Sep 95 00:00:09 -0400 From: polowin (Joel Polowin) To: Massimo Trotta Subject: Re: excel macros Cc: hyperchem@www > From: Massimo Trotta > Date: Tue, 5 Sep 1995 19:18:43 +0200 (MET DST) > > I've been trying to retrieving the phipsia.xlm Excel macro via WWW > connection. After a little struggling I was able to get the macro onto my > Hard disk. Unfortunately the file (which is 41834 bytes large) cannot be > opened by the Excel program. > In other words I'm stuck with this unopenable file. > Has anybody had a similar problem?: > I have an Excel 4.0 version that runs in Italian. Your WWW connection still isn't working properly. The "international" version of the macro -- which is the one you're trying to get -- is 43622 bytes in size. (The WWW page *says* that it's 44 kB.) The macro can also be grabbed by ftp from ftp.hyper.com, in the directory /pub/macros . Make sure you do a binary transfer. (I might venture a guess that your WWW server may not be transferring files in binary mode.) There is, of course, a simple solution: you could buy the ChemPlus package, which includes the macro... :-) Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 6 14:27:47 1995 From: "Deon Steyn" Organization: UOFS To: hyperchem@hyper.com Date: Wed, 6 Sep 1995 15:08:04 GMT+2 Subject: General Protection error? Can anybody help? I encountered an Application Error in Windows 3.1 when running a single point calculation on a molecule with the Molecular Print level set to 9 with a log file active. The error message is as follows: "CHEM 4 caused a general protection fault in module CHEM.EXE at 005:357D" I did define new atom types which consist of three letters eg. SMP, OMP, NMP, ect. Are there any names for new atom types that should be avoided? Regards Deon Steyn ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 6 21:15:03 1995 Date: Wed, 6 Sep 95 17:39:43 -0400 From: polowin (Joel Polowin) To: "Deon Steyn" Subject: Re: General Protection error? Cc: hyperchem@www > From: "Deon Steyn" > Date: Wed, 6 Sep 1995 15:08:04 GMT+2 > > I encountered an Application Error in Windows 3.1 when running a > single point calculation on a molecule with the Molecular Print > level set to 9 with a log file active. The error message is as > follows: > > "CHEM 4 caused a general protection fault in module CHEM.EXE at > 005:357D" > > I did define new atom types which consist of three letters eg. > SMP, OMP, NMP, ect. Are there any names for new atom types that > should be avoided? Three-letter atom types should be fine; the only things to avoid (that I know of) are duplicates of existing types (obviously). Things to check: * That you've entered all of the necessary data in the type/mass file for that force field * That the syntax of any modifications you've made to CHEM.RUL is correct * That you've compiled the parameter set after making any changes to the type/mass file or the rules file The most likely cause of trouble is something not quite right in the CHEM.RUL file. When I've created new atom types, I've found it most useful to add the new types to the end of the type/mass file, and to check my modifications after adding each new atom type by trying to use the new type in HyperChem. This makes it easier to find out where I've messed up when (*not* "if") I have trouble. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 11 16:42:30 1995 From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: hyperchem@hyper.com Date: Mon, 11 Sep 1995 16:51:24 GST Subject: automatic distance measurement Dear HyperChemists I am trying to write an Excel macro and/or HyperChem script that measures bond length's and angles. In the HyperChem handbooks I don't find the commands that - defines distances by selecting 2 predifined atoms or angles (torsion angles) by selecting 3 (4) atoms and then - write the corresponding value (length, angle or torsion angle) into an open log-file or the Excel table. Can somebody please give me an advice. Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 12 17:55:35 1995 Date: Tue, 12 Sep 95 10:14:17 -0400 From: polowin (Joel Polowin) To: "Gregor Fels" Subject: Re: automatic distance measurement Cc: hyperchem@www > From: "Gregor Fels" > Date: Mon, 11 Sep 1995 16:51:24 GST > > I am trying to write an Excel macro and/or HyperChem script that > measures bond length's and angles. In the HyperChem handbooks > I don't find the commands that > - defines distances by selecting 2 predifined atoms > or angles (torsion angles) by selecting 3 (4) atoms and then > - write the corresponding value (length, angle or torsion angle) into > an open log-file or the Excel table. > Can somebody please give me an advice. There are several options. First of all, you need to define a name for the group of atoms with Select/Name Selection; then the script command "select-name" can be used to select the atoms. Then "selection-value" can be used to return the numerical value of the selection -- length, angle, or torsion -- to external software. Also, one of our users discovered that "status-line", which is usually used as a command to print a message on the status line, can also be READ, and gives the last status message displayed. If you select a set of two, three, or four atoms, the status line immediately displays a description of the bond distance, angle, or torsion. With this message it is also possible to distinguish a bond distance from a non-bonded distance, or a bond angle from an improper angle (for example) since the messages displayed are different. To include these results in an open log file, for example JUNK.LOG, use the script command "append-omsgs-to-file junk.log". Using a command such as "query-value selection-value" would ordinarily cause the value to be displayed in a window as an OMSG, but now OMSGs are added to the specified file instead. The command "omsgs-not-to-file" restores the usual OMSG display. The "query-response-has-tag" command lets you specify whether the data values are preceded by the names of the values. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From polowin Tue Sep 12 19:35:17 1995 Date: Tue, 12 Sep 95 10:14:17 -0400 From: polowin (Joel Polowin) To: "Gregor Fels" Subject: Re: automatic distance measurement Cc: hyperchem@www > From: "Gregor Fels" > Date: Mon, 11 Sep 1995 16:51:24 GST > > I am trying to write an Excel macro and/or HyperChem script that > measures bond length's and angles. In the HyperChem handbooks > I don't find the commands that > - defines distances by selecting 2 predifined atoms > or angles (torsion angles) by selecting 3 (4) atoms and then > - write the corresponding value (length, angle or torsion angle) into > an open log-file or the Excel table. > Can somebody please give me an advice. There are several options. First of all, you need to define a name for the group of atoms with Select/Name Selection; then the script command "select-name" can be used to select the atoms. Then "selection-value" can be used to return the numerical value of the selection -- length, angle, or torsion -- to external software. Also, one of our users discovered that "status-line", which is usually used as a command to print a message on the status line, can also be READ, and gives the last status message displayed. If you select a set of two, three, or four atoms, the status line immediately displays a description of the bond distance, angle, or torsion. With this message it is also possible to distinguish a bond distance from a non-bonded distance, or a bond angle from an improper angle (for example) since the messages displayed are different. To include these results in an open log file, for example JUNK.LOG, use the script command "append-omsgs-to-file junk.log". Using a command such as "query-value selection-value" would ordinarily cause the value to be displayed in a window as an OMSG, but now OMSGs are added to the specified file instead. The command "omsgs-not-to-file" restores the usual OMSG display. The "query-response-has-tag" command lets you specify whether the data values are preceded by the names of the values. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 12 21:55:24 1995 Date: Tue, 12 Sep 95 19:11 GMT-0300 To: hyperchem@hyper.com From: burton@quimor.qo.fcen.uba.ar (Gerardo Burton) Subject: Gaussian type output Hi, is there a macro, program, etc that will modify an output from an ab initio calculation with Hyperchem 4.5 (logfile), so that it is compatible with the Gaussian format? I am using a program that requires as input a "standard Gaussian output" and the conversion doesn't seem to be straightforward. Any help will be appreciated Gerardo Gerardo Burton |Departamento de Quimica Organica burton@quimor.qo.fcen.uba.ar |Facultad de Ciencias Exactas y Naturales administrador del nodo |Universidad de Buenos Aires postmaster@quimor.qo.fcen.uba.ar |Tel/Fax 54 1 788-6915 ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Sep 15 20:59:37 1995 Date: Fri, 15 Sep 1995 15:03:00 -0700 To: hyperchem@hyper.com From: "J.L. Beauchamp" Subject: Problem with hardware lock I have just upgraded (?) my Pentium 100 (Triton chipset with on board IDE I/O) to Windows 95. I did a new installation and then installed other applications, including Hyperchem version 4.5. The dongle was originally on LPT1 (PCI high speed parallel port) and I got an error message "failure" to locate hardware lock. I moved it to LPT2 (ISA bus, printer card) and it let me generate and store two structures, recognizing the lock. I have shut off the computer, rebooted, and now neither port works with the dongle. Any suggestions? Jack Beauchamp J.L. Beauchamp California Institute of Technology 127-72 Pasadena, CA 91125 Phone: 818-395-6525 FAX: 818-568-8641 EMail: jlbchamp@cco.caltech.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 18 14:25:17 1995 From: Massimo Trotta Subject: references on nmr/molecular dynamic To: hyperchem@hyper.com Date: Mon, 18 Sep 1995 15:33:10 +0200 (MET DST) hallo everybody, I have a simple question: is there any references that I could get from generally available Journal about how to use molecular dynamics in simulating motions on the NMR time scale? What I have is a set of experimental correlation times that I wish to illustrate dynamically using Hyperchem 4.0. These times regard the sum of a tumbling and a rotational contribution to the overall correlation time of a moiety of a quinone copmpound; making certain assumption I can dived the contributes but it would be very convincing if I could run an experiment on hyperchem that gives these two correlation times or a related parameter. Thank you massimo trotta centro interazione luce-materia BARI ITALY csilmt12@area.ba.cnr.it ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 18 21:56:45 1995 Date: Mon, 18 Sep 95 18:00:00 -0400 From: polowin (Joel Polowin) To: "J.L. Beauchamp" Subject: Re: Problem with hardware lock Cc: hyperchem@www > Date: Fri, 15 Sep 1995 15:03:00 -0700 > From: "J.L. Beauchamp" > > I have just upgraded (?) my Pentium 100 (Triton chipset with on board IDE > I/O) to Windows 95. I did a new installation and then installed other > applications, including Hyperchem version 4.5. The dongle was originally on > LPT1 (PCI high speed parallel port) and I got an error message "failure" to > locate hardware lock. I moved it to LPT2 (ISA bus, printer card) and it let > me generate and store two structures, recognizing the lock. I have shut off > the computer, rebooted, and now neither port works with the dongle. Any > suggestions? It's quite strange for a setup like this to work for a while and then stop! The first thing to do, I think, is to test the port and the lock to make sure that they are both still working. Do you have a device such as a printer that you can try on the port, both with and without the lock present? (And you should see if having another device connected through the lock helps the lock to work.) Can you try installing the software and lock on a different computer to see if it works elsewhere? Is there any software that you installed between getting HyperChem to work and rebooting your system that would have been inactive until the reboot? (Are there now any tasks running concurrently with HyperChem that might be interfering in its finding the lock that were not running before?) Our tests with Win'95 have so far been quite positive; HyperChem and ChemPlus seem to work without any trouble -- as before, if Win'95 was installed on a system that had not previously had Windows. On some systems where Win'95 was installed over Windows, we are still seeing the problem that some script commands aren't recognised in HyperChem. We're still investigating this problem. In general, getting rid of all of the old Windows files before installing Win'95 seems to solve the problem. This doesn't sound like what you're reporting. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 19 16:18:14 1995 Date: Tue, 19 Sep 95 11:16:37 -0400 From: polowin (Joel Polowin) To: Massimo Trotta Subject: Re: references on nmr/molecular dynamic Cc: hyperchem@www > From: Massimo Trotta > Date: Mon, 18 Sep 1995 15:33:10 +0200 (MET DST) > > is there any references that I could get from generally available Journal > about how to use molecular dynamics in simulating motions on the NMR time > scale? > What I have is a set of experimental correlation times that I wish to > illustrate dynamically using Hyperchem 4.0. These times regard the sum of a > tumbling and a rotational contribution to the overall correlation time of a > moiety of a quinone copmpound; making certain assumption I can dived the > contributes but it would be very convincing if I could run an experiment on > hyperchem that gives these two correlation times or a related parameter. I don't think that this sort of thing is feasible. First of all, unless I'm mistaken, the NMR time scale is on the order of .0001--.001 seconds; this is much longer than the sub-picosecond time scale of molecular dynamics. There is also the potential problem that things like rotational effects at the molecular level depend on quantum-mechanical behaviour, whereas the atomic motions in our molecular dynamics calculations do not include quantum effects. (The forces on the atoms can be calculated with semi-empirical or ab initio methods, but the actual motions of the atoms are classical.) Obviously, if I'm mistaken in this, I'd like to know about it. A solution to this problem might go some way towards one of the limitations of HyperNMR: that it works only on static systems and that solvent effects can only be determined explicitly, by including a set of solvent molecules in the system. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 19 19:57:38 1995 Date: Tue, 19 Sep 95 16:51:50 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Re: references on nmr/molecular dynamic > Date: Tue, 19 Sep 95 11:16:37 -0400 > From: polowin (Joel Polowin) > > I don't think that this sort of thing is feasible. First of all, unless > I'm mistaken, the NMR time scale is on the order of .0001--.001 seconds; > this is much longer than the sub-picosecond time scale of molecular > dynamics. There is also the potential problem that things like rotational > effects at the molecular level depend on quantum-mechanical behaviour, > whereas the atomic motions in our molecular dynamics calculations do not > include quantum effects. (The forces on the atoms can be calculated with > semi-empirical or ab initio methods, but the actual motions of the atoms > are classical.) One of my colleagues just gave me a file of papers that involve molecular dynamics and NMR. Of these, the first seems closest to what Massimo Trotta was looking for: Giovanni Lipari, Attila Szabo, and Ronald M. Levy, "Protein dynamics and NMR relaxation: comparison of simulations with experiment". _Nature_, *300*, 197 (1982). R. Kapstein _et al._, "A Protein Structure from Nuclear Magnetic Resonance Data". _J. Mol. Biol._, *182*, 179 (1985). G. M. Clore _et al._, "Solution Conformation of a Heptadecapeptide Comprising the DNA Binding Helix F of the Cyclic AMP Receptor Protein of _Escherichia coli_". _J. Mol. Biol._, *186*, 435 (1985). Werner Braun, _Distance Geometry and related methods for protein structure determination from NMR data". _Quarterly Reviews of Biophysics_, *19*, 115 (1987). Michael Nilges _et al._, "Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2". _Protein Engineering_, *2*, 27 (1988). Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 21 16:44:48 1995 From: "Dr. Steven Desjardins" Organization: Washington & Lee University To: hyperchem@www Date: Thu, 21 Sep 1995 14:08:19 EDT Subject: Printed images Hi. How can I make hyperchem print pictures (like orbital contours) with thicker lines? I want to use some of these on a poster, but they are far too faint. Thanks, Steve Steven G. Desjardins Department of Chemistry Washington and Lee University Lexington VA 24450 (703) 463-8873 ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 21 21:40:56 1995 Date: Thu, 21 Sep 95 18:30:14 -0400 From: polowin (Joel Polowin) To: "Mceachern, Roderick" Subject: Re: Accuracy of Calculated Heats of Formation Cc: hyperchem@www > Date: Thu, 21 Sep 1995 13:25:00 -0500 (CDT) > From: "Mceachern, Roderick" > > Has anyone done a thorough study of the accuracy of heats of formation > calculated by HYPERCHEM? If so, what is the typical deviation between > calculated and experimental results? See J.J.P. Stewart's article "MOPAC: A Semiempirical Orbital Program" in _J. Computer-Aided Mol. Design_ *4*, 1 (1990) for a comparison of AM1 with experimental data. The original source papers for the semi-empirical methods, as referenced in _Computational Chemistry_, usually report these kinds of results as well. "Typical deviation" is awfully hard to pin down since this depends an awful lot on the set of structures which you select for your analysis. See the section "Energies of Molecules" in _Computational Chemistry_ -- p. 102 in the Release 4 for Windows book. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Fri Sep 22 05:45:53 1995 Date: Fri, 22 Sep 1995 08:50:36 +0200 (WET-DST) From: Francois Savary Subject: mail group question To: hyperchem@hyper.com Hello, Just a word to ask if it is possible to add automatically a keyword, e.g., HYPER: , to the subject line of the mails so to be able to screen rapidily through it. See you Francois ---------------------------------------------------------------------------- ------ Francois Savary, Ph.D. University of Geneva, Department of Applied Chemistry, Lab 112 CH-1211 Geneva 4 Switzerland voice : +4122 702 65 32 fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch WWW : http://scsg9.unige.ch/eng/toc.html (in English) http://scsg9.unige.ch/tabmat.html (en francais) http://scsg9.unige.ch/eng/cv.html (resume) http://scsg9.unige.ch/eng/pubdef.html (public defense of thesis) ---------------------------------------------------------------------------- ------ ________________________________________________________________________ From owner-hyperchem@hyper.com Sun Sep 24 22:39:25 1995 Date: Sun, 24 Sep 1995 23:39:18 +0100 To: hyperchem@hyper.com From: Jean-Francois Cordier Subject: n-butane study Hi All, We have to give a course on conformers and MM2 and I would like to use HyperChem to study the n-butane and cyclohexane conformers. Here's what I would like to do using a script: -rotate from 0 - 360 degree around the C2-C3 bond (torsion angle) and : *save the total energy of the molecule (every 10 degree, for instance) in a Excel spreadsheet -> nice graph. *save all energy contributions in the same spreadsheet. *save the molecule in PDB or MDL format (to render an animation). -do something similar using cyclohexane (maybe I could fix angles or distances and minimize the structure to get the chair and the boat conformers, any ideas?). I'm not very familiar with scripting, so if someone has already done something similar I'd appreciate help. I know I might use ChemPlus but we have only HyperChem 3 in the lab and HyperChem 4.5 (& ChemPlus 1.5) will be ordered only AFTER the course. Thanks a lot for the help, Jean-Francois. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 25 16:52:37 1995 From: Dragan Vuckovic Subject: HyperChem Workshop Announcement To: hyperchem@hyper.com Date: Mon, 25 Sep 1995 11:13:42 -0400 (EDT) ANNOUNCEMENT: Hypercube, Inc. presents an Introductory HyperChem Workshop on Computational Chemistry November 3-5, 1995 University of Guelph Guelph, Ontario, Canada HyperChem is like any other powerful tool: the more you know about it, the more you get out of working with it. For those who wish to learn more about the methods of molecular modeling and computational chemistry, about the ways of working with HyperChem, and about the range of problems you can now tackle on a PC, Hypercube, Inc. (the developers of HyperChem) offer an intensive three-day introductory workshop on molecular modeling with HyperChem. The workshop is pragmatic and application-oriented and makes no assumption of previous computational chemistry experience. Workshop Objectives The workshop will introduce you to techniques for working efficiently with HyperChem, provide a pragmatic user's guide to the scientific methods behind HyperChem, and include many hands-on exercises based on practical molecular modeling problems. Workshop Outline Day 1. Morning: Overview of Computational Chemistry Techniques; HyperChem Graphical Interface Afternoon: Molecular Mechanics Methods Laboratory session Day 2. Morning: Approximate and Semiempirical Molecular Orbital Methods; Ab initio Molecular Orbital Methods Afternoon: Frontier Orbital Theory: Examining Molecular Reactivity; Laboratory session Day 3. Morning: Molecular Dynamics; Molecular Spectroscopy; QSAR/Group Contribution Methods Afternoon: Laboratory session (optional) Costs and Venue The cost for the three-day course is $895 US (Academic and Government discount price is $ 695 US). For early registration (before October 20) the price is $ 795 US ( $ 595 US - academic). A limited number of special student discount fees at $ 295 US is available. This covers the cost of course materials, coffee, lunches and banquet dinner, and a PC to work on for the duration of the course (each participant will have their own machine). The number of participants is limited, so that extensive interaction with the workshop instructors is possible. Bring your own problems to work on during the course! The course will be held at the University of Guelph (O.V.C. Computer Lab, Room 2500), Guelph, Ontario, Canada. Reasonably-priced hotel accommodation is reserved for you at College Inn (on campus) should you wish. Also, please note if you are disabled or if there are any special food requirements. Workshop Instructors Dr. Neil S. Ostlund, Hypercube, Inc., Waterloo, Ont. Canada. Dr. Kenneth J. Tupper, Applied Research Corporation, Landover, MD USA Dr. Dragan Lj. Vuckovic, Hypercube, Inc., Waterloo, Ont. Canada. Registration To register for the course, please complete the form and return as soon as possible to: Dr. Dragan Lj. Vuckovic Hypercube, Inc. Unit 7, 419 Phillip Street Waterloo, Ont. Canada N2L 3X2 e-mail: vuckovic@hyper.com Tel. (519) 725-4040 Fax: (519) 725-5193 REGISTRATION FORM HyperChem Workshop on Computational Chemistry Guelph, Ontario, Canada November 3-5, 1995 Please reserve ____ spaces for the above workshop. NAME ______________________________________________________ ORGANIZATION ______________________________________________ POSITION __________________________________________________ ADDRESS FOR CORRESPONDENCE ____________________________________________________________ ____________________________________________________________ ____________________________________________________________ TEL. ____________ FAX _____________ E-MAIL _________________ Fees payable in advance: I enclose a check for $__________ US Please make your check payable to Hypercube, Inc. Please invoice me: Purchase Order Number __________________ VISA Card No: ____________________________ Exp. Date: _________ Cardholder: ________________________________ SIGNATURE ______________________ DATE ___________________ *Cancellation: If a participant cancels on or before October 27 (a week before the workshop), 50% of the workshop fee will be refunded. There will be no refunds for cancellations received after October 27, 1995. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 25 19:15:33 1995 Date: Mon, 25 Sep 95 14:58:56 -0400 From: polowin (Joel Polowin) To: Jean-Francois Cordier Subject: Re: n-butane study Cc: hyperchem@www > Date: Sun, 24 Sep 1995 23:39:18 +0100 > From: Jean-Francois Cordier > > We have to give a course on conformers and MM2 and I would like to use > HyperChem to study the n-butane and cyclohexane conformers. Here's what I > would like to do using a script: > > -rotate from 0 - 360 degree around the C2-C3 bond (torsion angle) and : > *save the total energy of the molecule (every 10 degree, for instance) in > a Excel spreadsheet -> nice graph. > *save all energy contributions in the same spreadsheet. > *save the molecule in PDB or MDL format (to render an animation). > > -do something similar using cyclohexane (maybe I could fix angles or > distances and minimize the structure to get the chair and the boat > conformers, any ideas?). Most of these things are already set up for you in the PHIPSI macro -- which, apart from being included in the ChemPlus package, is available for free download by ftp or WWW access. By ftp, it's on ftp.hyper.com, in /pub/macros; the file name is phipsi.xlm . Our WWW site is http://www.hyper.com , and the file is in the archives under 'Macros'. If members of this list have written macros which they think would be useful to others and which they are willing to share, we would (tentatively) be interested in making them available on our sites. If any of you would like to do this, please contact me directly (polowin@hyper.com). Running this sort of thing on a cyclic structure is much more difficult since you cannot use the set-bond-torsion or Model Builder commands on a torsional angle that is part of a ring. You can still constrain such an angle to a specified value (which takes effect when the Model Builder is run) and Model Build the *entire* structure. Or you can use a named restraint, which affects the structure when it is optimized, and simple let it minimize to the desired geometry. Another option would be to delete one bond from the ring so that the structure is no longer cyclic, set the torsion angle, then reconnect the atoms. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 25 20:10:35 1995 Date: Mon, 25 Sep 95 16:51:43 -0400 From: polowin (Joel Polowin) To: "Dr. Steven Desjardins" Subject: Re: Printed images Cc: hyperchem@www > From: "Dr. Steven Desjardins" > Date: Thu, 21 Sep 1995 14:08:19 EDT > > How can I make hyperchem print pictures (like orbital contours) with > thicker lines? I want to use some of these on a poster, but they are > far too faint. Hmm. If I save the picture as a metafile, then I can import that into other software; the final appearance depends on how the other software processes metafiles. For example, I can import it into CorelDraw, and then (with the metafile object selected) set the "pen width" to a heavier line. This thickens everything. I found that I had to "stretch" the object horizontally by 50% (i.e., reduce it to half its original width) to produce the same overall shape that I started with. If I save the picture as a bitmap and import it to Corel Photopaint, I can perform a variety of operations involving smoothing and sharpening the picture. I haven't yet found a way of broadening the "lines" of the image (actually a set of pixels, in a bitmap) that doesn't also make the lines fuzzy and faint. Anything that I do to make the lines more "solid" just seems to bring back the fine lines that I started with. I have found that if I am working in greyscale rather than in colour, I can blur the lines, and then repeatedly darken the picture (by about 20%) and increase the contrast, to make lines more solid. You might try importing the files into whatever software you have available, and seeing if your printer has control-panel options for line widths, to find out if the results from various combinations of options are more to your liking. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Mon Sep 25 22:19:41 1995 Date: Mon, 25 Sep 1995 22:34:11 GMT To: hyperchem (Joel Polowin) From: Vernon Anderson Subject: Re: Printed images At 04:51 PM 9/25/95 -0400, you wrote: >> From: "Dr. Steven Desjardins" >> Date: Thu, 21 Sep 1995 14:08:19 EDT >> >> How can I make hyperchem print pictures (like orbital contours) with >> thicker lines? I want to use some of these on a poster, but they are >> far too faint. In Paint SHop Pro (ver 3.11) apply the edge filter erode. This thickens all of the dark lines, maintaining the same color. ************************************************************* Vernon Anderson Department of Biochemistry Case Western Reserve University 10900 Euclid Ave., Cleveland, OH 44106-4935 Phone: 216-368-2599 FAX: 216-368-4544 ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 26 04:53:08 1995 Date: Mon, 25 Sep 1995 21:20:39 -0700 (PDT) From: Todd Whitcombe To: "Dr. Steven Desjardins" Cc: hyperchem@www Subject: Re: Printed images Steven, Further to all of the other suggestions, I just grabbed a bitmap and stuck it in the PaintBrush program that comes with Window. With a great deal of patience, you can re-color or shade atoms or thicken the lines. This is best achieved in the Zoom mode - so, yes, it is fiddly but produces nice results and if you happen to have a color printer... Cheers, Todd ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 26 16:03:23 1995 From: "Showalter, Steven K." To: "'HyperChem ListServer'" Subject: spin greater than 1/2 Date: Tue, 26 Sep 95 08:18:00 MDT Joel, Will the HyperNMR ever be able to do other nuclei? How about niobium or silicon? Steve skshowa@sandia.gov ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 26 19:54:06 1995 From: HUNNICUT@udavxb.oca.udayton.edu Date: Tue, 26 Sep 1995 16:18:40 -0400 (EDT) Subject: general information To: hyperchem@hyper.com I am interested in purchasing a molecular modelling program for use in research and for undergraduate lectures and labs. We have a multimedia overhead projection system which would be well-suited for some kind of modelling program. I would like to see the program used in as many of our classes as possible (not least because broad use justifies the expenditure), including general chemistry, organic chemistry, physical chemistry, and biochemistry. Has anyone one the list used hyperchem in lecture/lab? What advantages does Hyperchem have over other modelling programs which are available? Any comments/advice would be appreciated. Sally Hunnicutt Univ. of Dayton Dept. of Chem. hunnicut@udavxb.oca.udayton.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Tue Sep 26 23:15:50 1995 From: root@quimor.qo.fcen.uba.ar (root) Subject: printed images To: hyperchem Date: Tue, 26 Sep 1995 20:43:58 -0300 (GMT-0300) >Hi. > >How can I make hyperchem print pictures (like orbital contours) with >thicker lines? I want to use some of these on a poster, but they are >far too faint. > >Thanks, Steve > >Steven G. Desjardins >Department of Chemistry >Washington and Lee University >Lexington VA 24450 >(703) 463-8873 > > Hi An approach I have tried and appears to work fine is to import the drawing into Microsoft Word 2.0 (via the Windows clipboard), and then double click on it for editing with Microsoft Draw. Once it's in there and with all segments selected, you can change the line thickness (Draw/Line style/1 point, 2 point, etc), and then exit updating the picture. You may resize the drawing before printing directly from Microsoft Word Regards G. Burton Gerardo Burton |Departamento de Quimica Organica burton@quimor.qo.fcen.uba.ar |Facultad de Ciencias Exactas y Naturales administrador del nodo |Universidad de Buenos Aires postmaster@quimor.qo.fcen.uba.ar |Tel/Fax 54 1 788-6915 ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 27 16:07:21 1995 Date: Wed, 27 Sep 1995 07:46:46 -0700 To: hyperchem From: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: Re: printed images On this topic, I really need some rendering on the ribbon structures of proteins to give a more 3-D effect. Hyperchem's solid model pictures are really excellent with very good rendering but its ribbons are tacky. Any suggestions? -- Harry >>Hi. >> >>How can I make hyperchem print pictures (like orbital contours) with >>thicker lines? I want to use some of these on a poster, but they are >>far too faint. >> >>Thanks, Steve >> >>Steven G. Desjardins >>Department of Chemistry >>Washington and Lee University >>Lexington VA 24450 >>(703) 463-8873 >> >> Harry R. Matthews Professor of Biological Chemistry email hrmatthews@ucdavis.edu WWW home page http://moby.ucdavis.edu ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 27 16:25:39 1995 Date: Wed, 27 Sep 95 11:19:33 -0400 From: polowin (Joel Polowin) To: "Showalter, Steven K." Subject: Re: spin greater than 1/2 Cc: hyperchem@www > From: "Showalter, Steven K." > Date: Tue, 26 Sep 95 08:18:00 MDT > > Will the HyperNMR ever be able to do other nuclei? How about niobium or > silicon? "Ever"? Almost certainly. Things like being able to work on higher-atomic- number elements, and having more "types" for current elements such as P, are high on the list for future HyperNMR development. But that development has not yet been scheduled; I don't know *when* it is likely to happen. Silicon is within HyperNMR's current abilities but we haven't yet developed parameters so that it could be one of the active nuclei. If you wished to work on that, you would need to modify the *.ABP files, and probably the NMRTYPE.TXT and NMRTYPE.RUL files as well. Niobium would have to wait until HyperNMR is capable of handling transition metals -- and development of semi-empirical methods for transition metals, as a general field of research, has a *long* way to go. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 27 16:42:36 1995 From: "CHUNG TAT YIM" Organization: McGill University - Chemistry To: hyperchem@hyper.com (Joel Polowin) Date: Wed, 27 Sep 1995 12:14:43 EST5EDT Subject: Center of Mass Is there any easy way to find the location (i.e. coordinates) of center of mass in a molecular coordinate system? I have tried the following procedure but failed to move the center of mass to the origin of the coordinate system: a) Use "Align Viewer" to align the viewer's Z axis with molecular Z axis. b) Use "Align Molecules" to align primary and secondary inertial axes with X- and Y- axes. Careful examination of the results indicates that the intersection of the intertial axes is not at the origin of the coordinate system. C.T. Yim Chem. Dept., Dawson College, Montreal Canada E-mail Yim@omc.Lan.McGill.ca ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 27 17:09:09 1995 Date: Wed, 27 Sep 1995 08:48:07 -0700 To: HUNNICUT@udaVXB.oca.udayton.edu, hyperchem@hyper.com From: bolger@zygote.hsc.usc.edu (Michael B. Bolger, Ph.D.) Subject: Re: general information Sally, Hyperchem is excellent for research applications and modeling of both proteins and small molecules. It has very sophisticated minimization options. However, it is expensive. I think that the undergraduate (in my case Pharmacy professional) students benefit from hands on experience. Nobody can afford to buy that may copies of HyperChem. I suggest an excellent modeling program called "Molecules - 3D" that is inexpensive ($29.00) from Molecular Arts in Anaheim, CA (714-634-8100). This program has the ability to create molecular structures in two ways. First you can use what they call the Lewis Coach. This makes the students build a structure from atoms and electrons. They actually learn something about bonding. The second method is better for more complex models and involves building the structure by selecting atom types and hybridization. This program runs on both MAC and PC platforms so the students can use your computer lab facilities or buy their own copies. The graphics of this program are spectacular and easily copy from Molecules-3D into Word for report generation. Unfortunately, their molecular mechanics minimizer is practically useless. You need to correctly design the appropriate conformations with the building routines. HyperChem structure building is much less intuitive and educational. However, hyperchem has an interface with ISISDraw that allows the students to draw a structure in 2D (with stereochemistry indicated as hatched and wedges) then copy the 2D structure through the clipboard to HyperChem where it is accurately converted into a 3D structure. This is excellent for high throughput operations and is amenable to automation with macros or DDE scripts. However, HyperChem does not support MAC. The best of both worlds is where the instructor has one copy of HyperChem for structure optimization and the students learn and use Molecules-3D. Thats my opinion. At 04:18 PM 9/26/95 -0400, HUNNICUT@udavxb.oca.udayton.edu wrote: >I am interested in purchasing a molecular modelling program for use >in research and for undergraduate lectures and labs. We have a multimedia * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Michael B. Bolger, Ph.D. * Phone: (213) 342-1442 * * USC School of Pharmacy * FAX: (213) 342-1390 * * Dept. of Pharm. Sci. * Internet: bolger@zygote.hsc.usc.edu * * 1985 Zonal Ave. PSC 700 * * * Los Angeles, CA 90033 * * * U.S.A. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ________________________________________________________________________ From owner-hyperchem@hyper.com Wed Sep 27 21:10:46 1995 Date: Wed, 27 Sep 95 17:21:18 -0400 From: polowin (Joel Polowin) To: "CHUNG TAT YIM" Subject: Re: Center of Mass Cc: hyperchem@www > From: "CHUNG TAT YIM" > Date: Wed, 27 Sep 1995 12:14:43 EST5EDT > > Is there any easy way to find the location (i.e. coordinates) of > center of mass in a molecular coordinate system? The easiest way is to select the atoms or molecules whose centre of mass you wish to find, and use Select/Name Selection to give the special name POINT to the selection. Then if you open the Edit/Translate dialogue (or the Setup/Restraints dialogue, if you have another named selection) you can click on the item in the dialogue labelled POINT. The coordinates of POINT -- which is located at the centre of mass of that selection -- are shown in the display. Similarly, if you have a selection named LINE, you can use the Setup/ Set Velocity dialogue to determine the X, Y, and Z components of LINE -- that is, the best-fit line through that selection. > I have tried the following procedure but failed to move the center > of mass to the origin of the coordinate system: > a) Use "Align Viewer" to align the viewer's Z axis with molecular > Z axis. > b) Use "Align Molecules" to align primary and secondary inertial > axes with X- and Y- axes. > Careful examination of the results indicates that the intersection > of the intertial axes is not at the origin of the coordinate system. To move an object so that its centre of mass is at the origin of the molecular coordinate system, then all you have to do is select it, and use Edit/Translate to translate it to the origin. If the selection is only part of a molecule, you probably will want to make sure that "whole molecule translation" is turned on -- that's set under File/Tool Preferences. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 28 17:36:16 1995 Date: Thu, 28 Sep 95 11:22:47 -0400 From: polowin (Joel Polowin) To: hyperchem@www Subject: Updating ChemPlus to Release 1.5 First, I'd like to issue a reminder that registered users of ChemPlus 1.0 or 1.0A can update their software to ChemPlus 1.5. We do not charge for the update but we do charge for shipping it -- usually US$20 unless the actual shipping expenses are more than that. Your local dealer may be able to send you the update at lower cost. To arrange for getting the update from us, please write to our shipping manager, Irvine Nichols, by e-mail (nichols@hyper.com) or by fax (519-725-5193). You will need to send us your old ChemPlus serial number, and end-user name and address. If you have not previously registered your copy of ChemPlus, you will also need to send us the first page of the manual. There is a potential problem in installing ChemPlus 1.5 as an update to a previous installation of ChemPlus 1.0 or 1.0A. Most of the library files are marked as "read-only" to prevent their being changed accidentally, but this means that they also cannot be updated with new versions. If you wish to install ChemPlus to the same directory as before, you should first: 1. Use the Windows File Manager to find the subdirectory which contains the old ChemPlus files. (That subdirectory should be in the ChemPlus directory and should be named 'library'.) 2. Use the File Manager File/Select Files... dialog to select all of the files in that directory. 3. Use the File Manager File/File Properties... dialog to set the Attributes of those files: click on the check boxes until 'Read Only', 'Hidden', and 'System' are turned off (box is empty) and 'Archive' is turned on (box has an 'X' in it). Click on 'OK'. 4. Exit the File Manager (unless you wish to keep using it). Now you can install the new files over the old ones. The new files will be installed as "read-only" again. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 28 18:51:23 1995 Date: Thu, 28 Sep 95 14:58:50 -0400 From: polowin (Joel Polowin) To: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: Re: printed images Cc: hyperchem@www > Date: Wed, 27 Sep 1995 07:46:46 -0700 > From: hrmatthews@ucdavis.edu (Harry R. Matthews) > > On this topic, I really need some rendering on the ribbon structures of > proteins to give a more 3-D effect. Hyperchem's solid model pictures are > really excellent with very good rendering but its ribbons are tacky. Any > suggestions? Well, you *could* buy the SGI version of HyperChem -- which lets you specify either curved-line ribbons or solid ribbons, in any of the standard or user-defined colours. Apart from that -- other than the sorts of image manipulation that we have been discussing recently, I can't think of anything that you can do. The calculation of the 5-point 3D spline curve for the current display of ribbons for the Windows version of HyperChem is already a significant computational load, so improving it would not be easy. And, of course, we could not make any changes to the software until the next release. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself. ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 28 21:41:09 1995 Date: Thu, 28 Sep 1995 21:15:30 GMT To: hyperchem (Joel Polowin) From: Vernon Anderson Subject: Re: printed images The program RasWin makes very nice ribbon diagrams from pdb files. It will generate either strands or solid ribbons and in the beta release 2.6 it draws secondary structure "cartoons". I have used Hyperchem to make or later structures and RasWin to print them. Raswin has the added advantage of having depth cuing in its visualization. It can be downloaded from ftp.dcs.ed.ac.uk in the /pub/rasmol directory. ************************************************************* Vernon Anderson Department of Biochemistry Case Western Reserve University 10900 Euclid Ave., Cleveland, OH 44106-4935 Phone: 216-368-2599 FAX: 216-368-4544 ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 28 22:17:22 1995 Date: Thu, 28 Sep 1995 19:27:19 +0000 (GMT) From: Paddy Kane <94970459@vax1.dcu.ie> Subject: HyperChem and WINDOWS 95 To: hyperchem@hyper.com Hi HyperChemers, We plan to buy a pentium with WINDOWS 95. In recent messages to the user group Joel said has said that there are problems in running HyperChem under WINDOWS 95 if WINDOWS 95 has been installed on a computer which prevously had WINDOWS 3.1 (I don't know if that is the case with the computer which we are about to buy) but that there are no problems if the computer did not previously have WINDOWS 3.1. I would like to know what the experience of other users has been. Kind Regards, Paddy. Paddy Kane Dublin City University e.mail: 94970459@vax1.dcu.ie ________________________________________________________________________ From owner-hyperchem@hyper.com Thu Sep 28 22:26:52 1995 Date: Thu, 28 Sep 1995 14:29:59 -0700 To: hrmatthews@ucdavis.edu (Harry R. Matthews), hyperchem From: bolger@zygote.hsc.usc.edu (Michael B. Bolger, Ph.D.) Subject: Re: printed images Harry, Check out the free ware program RasMol. This is very good for ribbons as well as space fill representations. See following description. The complete source code and user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically. The loaded molecule may be shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. Atoms may also be labelled with arbitrary text strings. Different parts of the molecule may be displayed and coloured independently of the rest of the molecule or shown in different representations simultaneously. The space filling spheres can even be shadowed. The displayed molecule may be rotated, translated, zoomed, z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dials box. RasMol can read a prepared list of commands from a `script' file (or via interprocess communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally the rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage. RasMol will run on a wide range of architectures and systems including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBM RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available. The source code is public domain and freely distributable provided that the original author is suitably acknowledged. The complete source code and user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. The source code, documentation and Microsoft Windows executables are stored in several files appropriate for the receiving operating system. Please read the "README" file in the distribution directory. UNIX and VAX systems should retreive either RasMol2.tar.Z, RasMol2.tar.gz. Apple Mac users should retrieve RasMac.sit.hqx. Microsoft Windows users should retrieve RasWin.zip and optionally the Visual Basic package RasMenu.zip. All these files include source code, on-line help, user manual and reference card. RasMac.sit.hqx, RasWin.zip and RasMenu.zip also contain executables for the required platform. Please remember to use "binary" mode when transferring these files between systems. Check that the file size is the same before and after transfer. Any comments, suggestions or questions about the package may be directed to the author at "rasmol@ggr.co.uk". Roger -- Roger Sayle, INTERNET: ras32425@ggr.co.uk Glaxo Research & Development (GRD) ros@dcs.ed.ac.uk Greenford Road, Greenford Tel: (+44) 081 966 3567 (direct line) Middlesex UB6 0HE, UK. Fax: (+44) 081 966 4476 At 07:46 AM 9/27/95 -0700, Harry R. Matthews wrote: >On this topic, I really need some rendering on the ribbon structures of >proteins to give a more 3-D effect. Hyperchem's solid model pictures are >really excellent with very good rendering but its ribbons are tacky. Any >suggestions? * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Michael B. Bolger, Ph.D. * Phone: (213) 342-1442 * * USC School of Pharmacy * FAX: (213) 342-1390 * * Dept. of Pharm. Sci. * Internet: bolger@zygote.hsc.usc.edu * * 1985 Zonal Ave. PSC 700 * * * Los Angeles, CA 90033 * * * U.S.A. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ________________________________________________________________________ From polowin Fri Sep 29 00:11:09 1995 Date: Thu, 28 Sep 95 14:58:50 -0400 From: polowin (Joel Polowin) To: hrmatthews@ucdavis.edu (Harry R. Matthews) Subject: Re: printed images Cc: hyperchem@www > Date: Wed, 27 Sep 1995 07:46:46 -0700 > From: hrmatthews@ucdavis.edu (Harry R. Matthews) > > On this topic, I really need some rendering on the ribbon structures of > proteins to give a more 3-D effect. Hyperchem's solid model pictures are > really excellent with very good rendering but its ribbons are tacky. Any > suggestions? Well, you *could* buy the SGI version of HyperChem -- which lets you specify either curved-line ribbons or solid ribbons, in any of the standard or user-defined colours. Apart from that -- other than the sorts of image manipulation that we have been discussing recently, I can't think of anything that you can do. The calculation of the 5-point 3D spline curve for the current display of ribbons for the Windows version of HyperChem is already a significant computational load, so improving it would not be easy. And, of course, we could not make any changes to the software until the next release. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" (or "unsubscribe hyperchem") to hyperchem-request@hyper.com; please do not send such administrative messages to the group itself.