From slee@hyper Tue Mar 1 12:45:47 1994 From: slee@hyper.uucp (Thomas Slee) Subject: HyperChem e-mail list re-opening. To: hyperchem@HYPER.COM Date: Tue, 1 Mar 1994 12:36:02 -0500 ANNOUNCEMENT: HyperChem E-Mail List Re-opened ============================================= You may be aware that Hypercube has recently re-acquired the rights to sell and market HyperChem from Autodesk. I am sending the press release from Hypercube describing this transition in a separate message, and I hope the release answers most of your questions concerning the changeover. One consequence of the changeover is that the HyperChem e-mail list, which has been closed during the transition, has been moved to Hypercube. YOU HAVE BEEN AUTOMATICALLY ADDED TO THIS LIST. If you wish to stay on the list, you do not need to do anything. If you wish to unsubscribe, send a message to hyperchem-request@hyper.com containing the line: unsubscribe hyperchem There is a slightly different protocol for the list now, as the administration is being done automatically, rather than manually. The addresses relevant to the HyperChem e-mail list are as follows: To subscribe, unsubscribe, or get help: hyperchem-request@hyper.com For messages to the whole list: hyperchem@hyper.com For messages concerning the list: listadmin@hyper.com Here is the help file from hyperchem-request, which describes the commands this address understands. ----------------------------------------------------------------- hyperchem-request understands the following commands: subscribe [
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if specified) to the named . unsubscribe [
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if specified) from the named . which [
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if specified) are on. info Retrieve the general introductory information for the named . lists Show the lists served by this list server. help Retrieve this message. end Stop processing commands (useful if your mailer adds a signature). Commands should be sent in the body of an email message to "hyperchem-request@hyper.com". Commands in the "Subject:" line NOT processed. If you have any questions or problems, please contact "listadmin@hyper.com". ----------------------------------------------------------------- Welcome (back) to the HyperChem list. Tom Slee ________________________________________________________________________ From slee@hyper Tue Mar 1 13:19:22 1994 From: slee@hyper.uucp (Thomas Slee) Subject: HyperChem Press Release To: hyperchem@hyper.com Date: Tue, 1 Mar 1994 12:42:48 -0500 January 19, 1994 FOR IMMEDIATE RELEASE Hypercube to Market HyperChem: Re-acquires Rights from Autodesk WATERLOO, ONTARIO - Hypercube Inc. today announced that it had negotiated a mutual release from its comprehensive Development and License Agreement with Autodesk Inc., dating from July of 1990. The release returns the sales and marketing rights for HyperChem, which had been held by Autodesk, to Hypercube. The mutual release is effective immediately. "We are really excited about getting our products back," said Dr. Neil Ostlund, founder and CEO of Hypercube. "Autodesk helped us get started as a scientific software company, but their focus is really on Computer Automated Design (CAD). We recently launched a companion product to HyperChem called ChemPlus; its success helped convince me that it now makes more sense for us to market our own products." HyperChem is Hypercube's flagship molecular modeling product. Under the previous Development and License Agreement, Autodesk held an exclusive sales and marketing license to HyperChem. Release 2 of HyperChem was first shipped by Autodesk in March of 1992. The current Autodesk version of HyperChem, called Release 3, is sold world wide through distribution and reseller channels. Autodesk will continue to sell HyperChem Release 3 for a short interim period. Dr. Ostlund indicated that Hypercube should begin shipping its new Release 4 of HyperChem within 60 days and that it is expected to be sold through the same channels. "We've worked with Hypercube Inc. before." said John Offerman, the President of National Biosciences, a HyperChem distributor. "We're happy to see them take over the marketing of HyperChem. Their involvement and expertise could really help us." As a result of the new arrangement, Hypercube Inc. will be expanding its range of products and the range of platforms that are supported. "We are now free to market a number of products that we have been working on internally", said Dr. Robert Whiteside, VP of Engineering at Hypercube. "These may include networking, Unix, and NT versions of HyperChem as well as completely new products such as our about-to-be- released HyperNMR, an application for predicting the nuclear magnetic resonance spectra of molecules." Background ========== Hypercube is a privately held scientific software company incorporated in 1985. It previously built and sold turn-key molecular modeling systems that incorporated parallel processing. Its most recent software product is ChemPlus, a set of extensions to HyperChem, released in December of 1993. The company's technical expertise is centered at the boundary between computational chemistry and computer science. As the developer of HyperChem, Hypercube set new standards for ease of use and molecular modeling power on PC- based systems. Hypercube's goal is to bring scientific computing to tens of thousands of new customers. Autodesk is a public company with its headquarters in Sausalito, California. Its flagship product is AutoCAD, a computer-aided design product for engineers, architects and other designers. HyperChem is a molecular modeling software product noted for its ease of use. It is a comprehensive desktop productivity tool for visualizing, analyzing and communicating information about molecular structures. It is the most widely-used molecular modeling software for the Microsoft Windows environment of IBM-compatible PC's. HyperChem is a trademark of Hypercube, Inc. All other trade and product names mentioned are the service marks, trademarks or registered trademarks of their respective holders. ________________________________________________________________________ From uunet.ca!adfa.oz.au!apa@hyper Wed Mar 2 02:25:16 1994 Date: Tue, 1 Mar 1994 23:24:10 -0500 To: hyperchem@HYPER.COM From: adfa.oz.au!apa@hyper.uucp (Alan Arnold) Subject: Converting .snp files to movies? Can anyone tell me how to convert the contents of a .snp file to a more widely recognised animation format, say MPEG for Windows (or better - Quicktime for a Mac)? ---- Dr Alan Arnold, Chemistry Department, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2601 Australia voice:+61 6 268 8080 fax:+61 6 268 8002 e-mail: apa@adfa.oz.au web: http://ccadfa.cc.adfa.oz.au/CH/staff/apa.html ________________________________________________________________________ From uunet.ca!PSUVM.PSU.EDU!SOS1@hyper Wed Mar 2 09:16:25 1994 Date: Wed, 2 Mar 1994 08:23:00 -0500 From: "COMMAND" Subject: Re: Converting .snp files to movies? To: hyperchem@HYPER.COM Cc: hyperchem@HYPER.COM When is ChemPlus being released?????? ________________________________________________________________________ From uunet.ca!wuchem.wustl.edu!berger@hyper Wed Mar 2 14:33:56 1994 Date: Wed, 2 Mar 1994 14:16:37 -0500 From: wuchem.wustl.edu!berger@hyper.uucp To: "hyperchem@hyper.com"@WUGATE.wustl.edu Subject: Problem with ChemPlus Our recently-purchased copy of ChemPlus has a glitch: I am unable to import molecular orbitals which are generated with CI. Is that a common glitch, or am I doing something wrong? RHF and UHF-generated orbitals go into ChemPlus just fine. Dan Berger Department of Chemistry Washington University St. Louis MO 63130 berger@wuchem.wustl.edu ________________________________________________________________________ From uunet.ca!e154hf.tuwien.ac.at!jfroehli@hyper Thu Mar 3 02:28:57 1994 To: hyperchem@HYPER.COM Subject: hyperchem 4.0 ?? From: email.tuwien.ac.at!jfroehli@hyper.uucp (Dr. J. Froehlich) Reply-To: email.tuwien.ac.at!jfroehli@hyper.uucp Date: Thu, 3 Mar 1994 02:09:06 -0500 I have read something about hyperchem 4.0; when is it to be released, what features are new? *************************** Dr. J. Froehlich Org. Chem. TU Vienna jfroehli@email.tuwien.ac.at *************************** ________________________________________________________________________ From uunet.ca!e154hf.tuwien.ac.at!jfroehli@hyper Thu Mar 3 02:32:09 1994 To: hyperchem@hyper.com Subject: chemplus From: email.tuwien.ac.at!jfroehli@hyper.uucp (Dr. J. Froehlich) Reply-To: email.tuwien.ac.at!jfroehli@hyper.uucp Date: Thu, 3 Mar 1994 02:08:18 -0500 Hallo, *) has anybody written a macro or a script for HyperChem (or the like) which allows superimposing of some HIN-files (e.g. to present a family of conformers as a "bundle")? some comments: *) a message for german-speaking CHEMPLUS-users: this whole program does not work AT ALL, if you use the following number format (to be set in SYSTEM CONTROL of WINDOWS, and which is quite usual in the german- speaking world): e.g: 1.000,00 where , = comma; YOU HAVE TO USE: 1,000.00 (us style) instead --- you will find no warning for this in the manual of CHEMPLUS; this small difference is in fact the reason for many related problems: e.g.: difficulties with the phipsi-macro (after you have adopted some small "macro translation errors" regarding english/german EXCEL Version) also stem from wrong number format (see above); *) has anyone already some experience with "Conformation search" of ChemPlus; I would appreciate additional hints or an example with values for corresponding parameters; *) "Presentations" and "Orbital rendering" in ChemPlus is boring slow - is this generally to be observed? Thanks for comments, Johannes Froehlich ************************* Dr. Johannes Froehlich Inst. Organic Chemistry, Techn. Univ. Vienna Getreidemarkt 9 A-1060 VIENNA, AUSTRIA email.: jfroehli@email.tuwien.ac.at ************************* ________________________________________________________________________ From slee@hyper Thu Mar 3 14:14:18 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: Converting .snp files to movies? To: hyperchem@hyper.com Date: Thu, 3 Mar 1994 13:38:06 -0500 Alan Arnold writes... | | Can anyone tell me how to convert the contents of a .snp file to a more | widely recognised animation format, say MPEG for Windows (or better - | Quicktime for a Mac)? | There is currently no capability for this inside HyperChem, and in fact I don't know of any software for this purpose. I would be glad to hear of anything! Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From slee@hyper Thu Mar 3 14:14:36 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: ChemPlus To: SOS1@PSUVM.PSU.EDU (COMMAND) Date: Thu, 3 Mar 1994 13:41:51 -0500 Cc: hyperchem@HYPER.COM COMMAND writes... | | When is ChemPlus being released?????? | ChemPlus was released in December '93. For those of you who did not catch the announcement, ChemPlus is a set of extension modules for HyperChem that adds a variety of new functionality to the program. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From slee@hyper Thu Mar 3 16:33:01 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: chemplus To: jfroehli@email.tuwien.ac.at Date: Thu, 3 Mar 1994 14:08:30 -0500 Cc: hyperchem@HYPER.COM In reply to some of Dr. Froehlich's comments: | | *) a message for german-speaking CHEMPLUS-users: this whole program does not | work AT ALL, if you use the following number format (to be set in | SYSTEM CONTROL of WINDOWS, and which is quite usual in the german- | speaking world): e.g: 1.000,00 where , = comma; | YOU HAVE TO USE: 1,000.00 (us style) instead --- you will find no warning | for this in the manual of CHEMPLUS; | this small difference is in fact the reason for many related problems: | e.g.: difficulties with the phipsi-macro (after you have adopted some | small "macro translation errors" regarding english/german EXCEL Version) | also stem from wrong number format (see above); Dr. Froehlich is correct that HyperChem and ChemPlus do not communicate properly if the decimal separator is set to a comma in the Internationalization section of the Control Panel. The reason is not what Dr. Froehlich suggests, however. In fact, ChemPlus does observe the internationalization settings. However, HyperChem forces output of numbers using a period as decimal separator, so that ChemPlus looks for commas and does not find them, hence the problem. There are problems going both ways: if HyperChem obeyed the internationalization settings then HIN files would not be exchangeable between countries using different conventions, for instance. | *) "Presentations" and "Orbital rendering" in ChemPlus is boring | slow - is this generally to be observed? Presentations is indeed much slower than HyperChem in its renderings. Presentations is intended to produce high quality images, and in choices between speed and quality we have opted here for quality. One could speed the renderings up at the cost of some quality, indeed if you look in the HCMP.INI file in your Windows directory you can alter the quality of the screen image. Our rough separation is that HyperChem provides working graphics, whereas Presentations provides presentation graphics. Yours, Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uunet.ca!JCVAXA.JCU.EDU!EWING@hyper Fri Mar 4 20:03:16 1994 Date: Fri, 4 Mar 1994 15:30:00 -0500 From: "DAVID W. EWING (216) 397-4742" Subject: Printing labels To: hyperchem@HYPER.COM I cannot get chemical symbols to print (plot). I've tried changing the PrintLevel in the chem.ini file, but to no avail. Please advise. (I'm still using version 2.) Thanks! Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu ________________________________________________________________________ From uunet.ca!VTBIT.CC.VT.EDU!VM.LNCC.BR!VM.LNCC.BR!CCATF@hyper Sat Mar 5 22:14:06 1994 Date: Thu, 3 Mar 1994 06:51:30 -0500 From: VTBIT.CC.VT.EDU!CCATF%BRLNCC.BITNET@hyper.uucp To: HYPERCHEM@HYPER.COM Dear hyperchem<: whem will hyperchem 4.0 be released. dr. c. a. taft ________________________________________________________________________ From uunet.ca!duq3.cc.duq.edu!TAMINE@hyper Thu Mar 10 20:13:23 1994 Date: Thu, 10 Mar 1994 19:18:52 -0500 From: duq3.cc.duq.edu!TAMINE@hyper.uucp To: hyperchem@HYPER.COM Subject: radicals I am a beginner at HyperChem. Could anyone tell me how to create an organic structure in HC that has a carbon-centered free radical in it, if possible. Thanx, John Tamine Duquesne University Pittsburgh, PA ________________________________________________________________________ From uunet.ca!IJS.si!Joze.Koller@hyper Fri Mar 11 04:09:24 1994 Date: Fri, 11 Mar 1994 02:54:55 -0500 From: IJS.si!Joze.Koller@hyper.uucp To: HYPERCHEM@HYPER.com Subject: some questions Hi ! As a beginner in HC I met some problems using Z-matrix file filter. Can someone help me? - Must the input file (*.ZMT) start with blank line ? - How to succeed that two atoms will be automatically connected at the distance which is somewhat longer that the standard one? Thanks for the answers! Joze Koller University of Ljubljana Slovenia ________________________________________________________________________ From uunet.ca!esseX.stfx.ca!klapstein@hyper Fri Mar 11 14:11:12 1994 Date: Fri, 11 Mar 1994 12:31:42 -0500 From: esseX.stfx.ca!klapstein@hyper.uucp To: hyperchem@HYPER.COM Subject: Hyperchem&Pentium While I thoroughly enjoy the many features of Hyperchem, at times I spend a lot of time waiting, especially for large molecule geometry optimizations, and calculation of spectra, and the ChemPlus orbital visualizations. All of these are, of course, CPU intensive operations. The new Pentium PCs appear to offer much faster calculations, based on the ads. Now I would like to get some feedback from people who have run HyperChem on say, 486-66 PCs and P5 based PCs. Is there a "quantum" leap in performance for Hyperchem to justify the associated quantum leap in price, or should I stick with my 486 machine? Dieter Klapstein St. Francis Xavier University Antigonish, Nova Scotia, Canada. ________________________________________________________________________ From uunet.ca!IJS.si!Joze.Koller@hyper Fri Mar 11 14:11:14 1994 Date: Fri, 11 Mar 1994 11:27:20 -0500 From: IJS.si!Joze.Koller@hyper.uucp To: HYPERCHEM@hyper.com Subject: once again!! Hi ! As a beginner in HC I met some problems using Z-matrix file filter. Can someone help me? - Must the input file (*.ZMT) start with blank line ? - How to succeed that two atoms will be automatically connected at the distance which is somewhat longer that the standard one? Thanks for the answers! Joze Koller University of Ljubljana Slovenia ________________________________________________________________________ From uunet.ca!asnc90.asc.edu!aubmes01@hyper Fri Mar 11 16:26:19 1994 Date: Fri, 11 Mar 1994 14:30:47 -0500 Apparently-To: HYPER.COM!hyperchem@bobino.BRI.NRC.CA From: To: Gaussian92 has a utility called FREQCHK which is advertised to take frequency information from a gaussian chkpoint file and convert it into a script file that can be used by HYPERCHEM to display and animate the vibrations. This appears to work, but in fact does not in that the displayed vibrations, at least the ones I have tried, are not animated correctly. Symmetric vibrations are not symmetric, etc. The script file generated by FREQCHK looks OK. Anybody else have this problem? Does anyone know what might be going on? The frequencies I examined were mostly negative frequencies of some calculated transition states. Mike Squillacote ________________________________________________________________________ From uunet.ca!ALIJKU11.EDVZ.Uni-Linz.AC.AT!jk.uni-linz.ac.at!nmueller@hyper Fri Mar 11 16:32:55 1994 Date: Fri, 11 Mar 1994 14:37:52 -0500 To: hyperchem@HYPER.COM From: jk.uni-linz.ac.at!nmueller@hyper.uucp (Norbert Mueller) Subject: Re: Hyperchem&Pentium Cc: klapstein@essex.stfx.ca >While I thoroughly enjoy the many features of Hyperchem, at times I spend >a lot of time waiting, especially for large molecule geometry optimizations, >and calculation of spectra, and the ChemPlus orbital visualizations. All of >these are, of course, CPU intensive operations. The new Pentium PCs appear >to offer much faster calculations, based on the ads. Now I would like to >get some feedback from people who have run HyperChem on say, 486-66 PCs >and P5 based PCs. Is there a "quantum" leap in performance for Hyperchem >to justify the associated quantum leap in price, or should I stick with >my 486 machine? > >Dieter Klapstein >St. Francis Xavier University >Antigonish, Nova Scotia, Canada. I still cannot understand why they gave up the SGI platform.... But a move to the PPC would also be nice. (but I am a Mac person) ---------------------------------------------------------------- Norbert Mueller - Institut f. Chemie, Johannes Kepler University A-4040 Linz Austria e-mail: NMUELLER@jk.uni-linz.ac.at (POP3 - Eudora - preferred) Norbert@soft.uni-linz.ac.at (MacPost - for personal messages) norbertm@convex.edvz.uni-linz.ac.at (unix - for BIG files) ________________________________________________________________ "True science teaches, above all, to doubt, and to be ignorant." Miguel do Unamuno ________________________________________________________________________ From uunet.ca!marshall.wvnet.edu!CHM010@hyper Fri Mar 11 23:34:22 1994 Date: Fri, 11 Mar 1994 22:36:00 -0500 From: "Gary D. Anderson" Subject: How to convert .snp files to movies for PC or Mac To: hyperchem@hyper.com Alan Arnold writes... | | Can anyone tell me how to convert the contents of a .snp file to a more | widely recognised animation format, say MPEG for Windows (or better - | Quicktime for a Mac)? | >There is currently no capability for this inside HyperChem, and in >fact I don't know of any software for this purpose. I would be glad >to hear of anything! > Tom Slee - I have been working with Todd Wipke at University of California-Santa Cruz and we have developed a set of programs that allows the display of movies on any PC (even an 8088 with CGA -- slow as molasses on an 8088 but works ok for small molecules, reasonable speed on a 12 MHz 80286 for moderate size molecules and quite acceptable for fairly large molecules on 386 or 486 -- can actually play the animation faster that the standard Hyperchem movie playback) or any Mac (Mac Plus or better). The package is called MAGIC (Mailable Animation Generator with Interpolation and Compression). There are four modules in the package. The first three modules are only for MSDOS but the MIRRORS module works on both the PC and the Mac HOCUS -- this module reads Hyperchem .snp and .hin files or Discover Insight .his and .mdf files to generate a straight ascii file that we call a .hat file. This file contains all of the connection table data and all of the coordinate data for the movie. This is the only module that is specific to any method or platform for generating the movie and we are working on the ability to read other types of movie files. POCUS -- this module allows "editing" of the .hat file. You can select certain portions of the data for display instead of having to play the entire movie. SMOKE -- this module reads our .hat files and produces a special compressed ascii file known as an .ash file. The .ash file is a 7-bit ascii file that can be sent via e-mail without any problems. No line is longer that about 65 characters and it can be split into multiple files for long movies. We have tested one data set by mailing it around between 6 or 7 systems running including Sun, Vax, and Convex systems until the mail headers were 1/3 of the total file length and the file was still usable without any hand editing. This module also allows the user to select color and relative size assignments for each atom. A movie for a medium sized molecule such as latrunculin (approx 60 atoms) with approximately 100 sets of coordinates for each atom is 65K in length. MIRRORS -- this is the actual movie display module and we have versions for both MSDOS and Mac. It reads the .ash files, automatically stripping out any mail headers and doing some fairly extensive checking for file integrity. It then proceeds to display the movie in a continuous loop, reversing directions when it reaches the end of the movie. We get smoother animation by interpolating between the actual coordinates in the data set and the user can "speed up" or "slow down" the movie by changing the number of interpolations being performed. We have color coded ball and stick, element symbol ball and stick, atom number ball and stick, and wireframe display modes. We also have a "time lapse" display mode where we do not erase the previous images but just display the new postions on top of the old. This is very useful in pinpointing the portions of the molecule with the greatest motion. There are a number of other user controllable display options including "freeze frame", reverse direction, rotation, scaling, translation, toggling the display of hydrogen atoms and other selected atoms ... We also can generate a .MOL file for any frame and from any viewpoint so that we can get a snapshot for inclusion in programs like ChemText, Isis Draw, ChemDraw, ChemIntosh, etc. Gary D. Anderson Professor of Chemistry Marshall University Huntington, WV 25755 chm010@marshall.wvnet.edu ________________________________________________________________________ From uunet.ca!mitr.p.lod.edu.pl!sopekmir@hyper Mon Mar 14 16:09:59 1994 From: mitr.p.lod.edu.pl!sopekmir@hyper.uucp (Miroslaw Sopek) To: hyperchem@HYPER.COM Subject: HIN -> 3D studio Date: Mon, 14 Mar 1994 14:17:03 -0500 Hello, Do you know something about READY TO USE program that converts HyperChem structures to the AutoDesk 3D studio file format (3DS, ASC, DXF or something else) ? I have written something but it seems that it do not satisfies me, and I had to animate something urgently, Miroslaw Sopek, Phd sopekmir@mitr.p.lod.edu.pl ________________________________________________________________________ From slee@hyper Fri Mar 18 13:22:32 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: Z matrix format. To: Joze.Koller@IJS.si Date: Fri, 18 Mar 1994 12:58:24 -0500 Cc: HYPERCHEM@HYPER.COM Joze.Koller@IJS.si writes... | | As a beginner in HC I met some problems using Z-matrix file | filter. Can someone help me? | - Must the input file (*.ZMT) start with blank line ? It does not need to start with a blank line, but must follow the standard MOPAC format, which is: Line 1: Keywords. (These are ignored by HyperChem, which is why it is left blank in ZMT files we write out.) Lines 2 and 3: Comment lines Lines 4 on: molecule specification. | - How to succeed that two atoms will be automatically | connected at the distance which is somewhat longer that the | standard one? If you are using the model builder, you can select the two atoms of interest, and then use the constrain bond length setting in the Build menu to force them close to the length you want. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From slee@hyper Fri Mar 18 13:22:35 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: Hyperchem&Pentium To: klapstein@esseX.stfx.ca Date: Fri, 18 Mar 1994 13:02:25 -0500 Cc: hyperchem@hyper.com Dieter Klapstein writes... | While I thoroughly enjoy the many features of Hyperchem, at times I spend | a lot of time waiting, especially for large molecule geometry optimizations, | and calculation of spectra, and the ChemPlus orbital visualizations. All of | these are, of course, CPU intensive operations. The new Pentium PCs appear | to offer much faster calculations, based on the ads. Now I would like to | get some feedback from people who have run HyperChem on say, 486-66 PCs | and P5 based PCs. Is there a "quantum" leap in performance for Hyperchem | to justify the associated quantum leap in price, or should I stick with | my 486 machine? | Our experience, like many others, is that the speedup between the 486-66 and a Pentium is pretty close to a factor of two. Whether you want to switch or not is, of course, up to you. Yours Tom -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uunet.ca!doane.edu!dsmith@hyper Mon Mar 21 19:24:39 1994 Date: Mon, 21 Mar 1994 18:06:45 -0500 From: doane.edu!dsmith@hyper.uucp To: hyperchem@hyper.com Subject: heats of formation I am a novice at computational chemistry. Hyperchem looks like a nifty tool to use to look at some long-standing questions, but I quickly find I don't know enough to find what I want in the manual. So, HELP! I am running HyperChem Release 2 on a 386 4meg 16MHz machine, with a math card, your minimum configuration. 1. Heat of formation. I understand that for the "steric energy" of two different non-isomeric molecules to be compared, the "steric energy" must first be transformed to heat of formation, and that the computational methods hyperchem uses, MM+, AM1, etc, will produce such a heat. Nowhere on the out- put log or elsewhere do I find something overtly called "heat of formation". A bulletin board message back in November showed where the conversion factors can be found that allow heat of formation to be calculated from AM1 results. Great, but my life expectancy is shorter than the run time of AM1 on my machine and my molecule. How can I get heat of formation from MM+? 2. I'd love to be able to dock simple (sophomore organic sized) molecules. I find references to doing this in the manual, but no directions. How? 3. Our only color hard-copy device is an HP Color Pro plotter. Can hyper- chem drive that device? How? Thanks for any help you can give, including references. Dave Smith Doane College Crete Ne dsmith@doane.edu Thanks for any help you can give. ________________________________________________________________________ From uunet.ca!NAUVAX.UCC.NAU.EDU!NGR@hyper Mon Mar 21 19:25:22 1994 Date: Mon, 21 Mar 1994 18:29:00 -0500 From: Nate the Great Subject: Education To: hyperchem@hyper.com I am interested in finding out from professors if they use HyperChem in their classroom, or if they would if there was a way of automating it to do demonstrations. The main application that I have in mind is that of different conformation of alkanes and the energies calculated by these different conformations. I would appriciate any and all response to my E-mail address: Nathan Raper NGR@NAUVAX.UCC.NAU.EDU ________________________________________________________________________ From uunet.ca!gandalf.otago.ac.nz!DSCHMIERER@hyper Tue Mar 22 02:15:04 1994 To: hyperchem@HYPER.COM From: gandalf.otago.ac.nz!DSCHMIERER@hyper.uucp Organization: University of Otago Date: Tue, 22 Mar 1994 13:09:08 -0500 Subject: FAQs These questions come from myself as well as some other staff and students. They were previously posted when the Users' group was undergoing re-structuring. I have not seen them posted and I'm not sure if they even got out of the University 1. When a 2D free-drawn object is converted to a 3D object (by invoking model builder) the position of the molecule changes radically from the approximate position of the 2D object. It seems to flip by about 90 to 180o as well as twist a little. This is not always a consistent occurrence, but can cause some confusion, especially with more complex molecules. Also, it is a nuisance to draw a molecule approximately the way you want to view it, and then have to go through further steps to achieve this after model building. Is this *normal*? 2. The aromatic ring, for example benzene, is represented by a hexagon with six joined dotted lines. Why are five of these dotted lines on the inside of the hexagon and the sixth on the outside of the hexagon? It almost seems to be a 3D effect, with five of the dotted lines being above the plane of the ring and the sixth below the plane of the ring. 3. We use 33MHz PC clone 486s with SVGA and 4Mb of RAM as a standard configuration. When manipulating a translated PDB file we noticed that this is particularly slow. This can cause some problems for students and staff, as they often try to repeat a manipulation when this is already in process, leading to a double manipulation. Is this problem able to be solved by putting more in the system (RAM or SVGA)? 4. We like ChemPlus, although we can see some limitations in the QSAR section. In one of your previous releases, you mentioned the imminent release of HyperChem version 4 and an NMR simulating programme. Is there any further news on these? David M. Schmierer School of Pharmacy University of Otago Dunedin, New Zealand Fax: 64 3 479 7034 Voice: 64 3 479 7289 E-mail: dschmierer@gandalf.otago.ac.nz ________________________________________________________________________ From slee@hyper Wed Mar 23 04:09:07 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: FAQs To: DSCHMIERER@gandalf.otago.ac.nz Date: Tue, 22 Mar 1994 13:16:53 -0500 Cc: hyperchem@hyper.com DSCHMIERER@gandalf.otago.ac.nz writes... | | 1. When a 2D free-drawn object is converted to a 3D object (by invoking | model builder) the position of the molecule changes radically from the | approximate position of the 2D object. It seems to flip by about 90 | to 180o as well as twist a little. This is not always a consistent | occurrence, but can cause some confusion, especially with more | complex molecules. Also, it is a nuisance to draw a molecule | approximately the way you want to view it, and then have to go through | further steps to achieve this after model building. Is this *normal*? | | 2. The aromatic ring, for example benzene, is represented by a | hexagon with six joined dotted lines. Why are five of these dotted lines | on the inside of the hexagon and the sixth on the outside of the | hexagon? It almost seems to be a 3D effect, with five of the dotted | lines being above the plane of the ring and the sixth below the plane of | the ring. Both these design decisions were taken long ago, by people no longer with the company. Your questions will prompt us to look again at these choices, as there does not seem to be definite rationales for either. If you find the viewing angle chosen by the model builder confusing, one workaround may be to have a short script available which finds a suitable viewing angle. Here is one possibility: ; Align.scr: produces a standard alignment of a molecule select-none align-viewer z align-molecule primary, x, secondary, y menu-select-select-all translate-selection 0,0,0 select-none You could incorporate this into your Script menu automatically by making a file chem.scr in your HyperChem directory (which is run automatically on start up, if it exists) which says change-user-menuitem 1, "Standard Alignment", c:\hyper\align.scr where you have the explicit path for your file in the command. | | 3. We use 33MHz PC clone 486s with SVGA and 4Mb of RAM as a | standard configuration. When manipulating a translated PDB file we | noticed that this is particularly slow. This can cause some | problems for students and staff, as they often try to repeat a | manipulation when this is already in process, leading to a double | manipulation. Is this problem able to be solved by putting more in the | system (RAM or SVGA)? First, you will find that rotations are speeded up if you simplify the display: clearing hydrogen atoms off the display and not showing multiple bonds are two easy ones, you could also select the interesting parts of molecules and use the Show Selection Only command to cut down the complexity of the display. Second, the graphics card speed is important. SVGA as opposed to VGA will slow down the rendering if anything (more pixels to draw). RAM won't help this problem much by itself: it's all in the graphics card. | | 4. We like ChemPlus, although we can see some limitations in the | QSAR section. In one of your previous releases, you mentioned the | imminent release of HyperChem version 4 and an NMR simulating | programme. Is there any further news on these? | There will be an announcement on this list shortly (within a week) on this topic. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From slee@hyper Wed Mar 23 04:20:47 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: HIN -> 3D studio To: sopekmir@mitr.p.lod.edu.pl (Miroslaw Sopek) Date: Tue, 22 Mar 1994 13:41:35 -0500 Cc: hyperchem@hyper.com Miroslaw Sopek writes... | | Hello, | Do you know something about READY TO USE program | that converts HyperChem structures to the AutoDesk 3D studio | file format (3DS, ASC, DXF or something else) ? | There is a public domain program by the name of CineChem that I can send in uuencoded form to interested people. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From slee@hyper Wed Mar 23 04:38:06 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: heats of formation To: dsmith@doane.edu Date: Tue, 22 Mar 1994 14:05:20 -0500 Cc: hyperchem@hyper.com dsmith@doane.edu writes... | | I am running HyperChem Release 2 on a 386 4meg 16MHz machine, with a math | card, your minimum configuration. | | 1. Heat of formation. I understand that for the "steric energy" of two | different non-isomeric molecules to be compared, the "steric energy" must | first be transformed to heat of formation, and that the computational methods | hyperchem uses, MM+, AM1, etc, will produce such a heat. Nowhere on the out- | put log or elsewhere do I find something overtly called "heat of formation". | Great, but my life expectancy is shorter than the run time of AM1 on my | machine and my molecule. How can I get heat of formation from MM+? The heat of formation is produced by AM1 and recorded in the log file. There is no heat of formation produced by MM+, unfortunately. | | 2. I'd love to be able to dock simple (sophomore organic sized) molecules. | I find references to doing this in the manual, but no directions. How? I'll post a short note on this to the general list in a couple of weeks. The procedure in outline is to do a restrained optimization of one molecule while keeping the other molecule fixed. 1. Select two atoms (one in each molecule) which you know are close together. 2. Name the selection, eg. "Dock" using Select / Name Selection... 3. Apply a constraint (in the options of the force field method box) to fix the value of "Dock" to an appropriate distance, with a large force constant (say 50). 4. Select just one of the two molecules, leaving the other unselected. 5. Carry out an optimization: the selected atoms only are allowed to move, and they include the constraint. | | | 3. Our only color hard-copy device is an HP Color Pro plotter. Can hyper- | chem drive that device? How? Plotters are generally not supported in Windows. You may be able to send sticks renderings to the plotter, but you won't be able to send spheres to it. Most Windows print functions assume some sort of raster device. I hope these remarks help, Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uunet.ca!ibmmail.IBMMAIL.COM!usech592@hyper Wed Mar 23 23:30:15 1994 Date: Wed, 23 Mar 1994 09:16:26 -0500 From: ibmmail.COM!usech592@hyper.uucp To: hyperchem@HYPER.COM Subject: PDB dihedral defaults ----------------------- Mail item text follows --------------- To: INTERNET--IBMMAIL Internet Communica From: John C. Hubbs, Chemistry Research Division, B-150B Subject: PDB dihedral defaults I recently loaded into hyperchem (ver 3) a prepublication version of a PDB file which contained sequence information and c-alpha positions. This particular file stated that a later release would provide the remaining atomic coordinates. Much to my suprise, hyperchem provided a complete 3-D display of the entire protein. I imagine that the backbone is uniquely defined by sequence and C-alpha information alone. How are the side chain dihedrals chosen? P.S.: I find the display of biological molecules to be a particular strength of hyperchem. Good luck with your continued development of this product. John Hubbs ________________________________________________________________________ From slee@hyper Wed Mar 23 23:37:57 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: PDB dihedral defaults To: hyperchem@HYPER.COM Date: Wed, 23 Mar 1994 16:35:18 -0500 John Hubbs writes... | I recently loaded into hyperchem (ver 3) a prepublication version of a PDB | file which contained sequence information and c-alpha positions. This | particular file stated that a later release would provide the remaining atomic | coordinates. Much to my suprise, hyperchem provided a complete 3-D display of | the entire protein. I imagine that the backbone is uniquely defined by | sequence and C-alpha information alone. How are the side chain dihedrals | chosen? Given alpha carbon positions only for a set of know residues, HyperChem will fill in the rest of the atoms in each residue and place them on the screen. However, the backbone angles will NOT be good ones, unfortunately. The general problem of filling in a protein structure from the alpha carbon positions is one that has received some attention in recent research, and it is not an easy one. In fact, I know of somebody who has tried to develop a method of doing this using HyperChem (who is on this list and may wish to provide some comments...). Sorry if it is disappointing that the backbone is not a realistic one. Yours Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ________________________________________________________________________ From uunet.ca!cv1.chem.purdue.edu!john@hyper Mon Mar 28 08:23:52 1994 Date: Mon, 28 Mar 1994 07:08:48 -0500 From: cv1.chem.purdue.edu!john@hyper.uucp (John J. Nash) To: hyperchem@hyper.com Subject: EHMO parameters beyond Xenon Dear Netters, We are interested in using Hyperchem to do some Extended Huckel calculations on compounds containing gold. Hyperchem gives an error message whenever an element beyond xenon is used. Is there any way to use elements beyond xenon in Hyperchem? Also, the manual discusses "phoney fluorines" in the Extended Huckel parameter file. Could someone enlighten me as to what a "phoney fluorine" is? Is this a carbon atom in disguise? John Nash Purdue University Department of Chemistry W. Lafayette, IN 47907 john@cv1.chem.purdue.edu ________________________________________________________________________ From slee@hyper Mon Mar 28 11:29:12 1994 From: slee@hyper.uucp (Thomas Slee) Subject: Re: EHMO parameters beyond Xenon To: hyperchem@hyper.com Date: Mon, 28 Mar 1994 10:56:38 -0500 John J. Nash writes... | | We are interested in using Hyperchem to do some Extended Huckel | calculations on compounds containing gold. Hyperchem gives an error | message whenever an element beyond xenon is used. Is there any way | to use elements beyond xenon in Hyperchem? HyperChem does not currently support elements beyond Xenon for semi-empirical calculations, so there is no way of using these elements for Extended Huckel calculations. | | Also, the manual discusses "phoney fluorines" in the Extended Huckel | parameter file. Could someone enlighten me as to what a "phoney | fluorine" is? Is this a carbon atom in disguise? "Phoney fluorine atoms" appear in HyperChem's treatment of selected parts of a molecule by semi-empirical methods. These are the bounding atoms of the selected portion. You can find documentation of the method in the Computational Chemistry manual, Theory and Methods section, p 87 and on. Also, New Features p 54 and on. Yours Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040