From Jeffrey.Gosper@brunel.ac.uk Mon Aug 8 04:30:39 1994 Received: from sirius.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id EAA03384; Mon, 8 Aug 1994 04:08:36 -0400 Received: from molnir.brunel.ac.uk by sirius.brunel.ac.uk with SMTP (PP) id <03670-0@sirius.brunel.ac.uk>; Mon, 8 Aug 1994 09:13:56 +0100 From: Jeffrey J Gosper Message-Id: <6272.9408080813@molnir.brunel.ac.uk> Subject: Xmol and VIBRAM To: CHEMISTRY@ccl.net Date: Mon, 8 Aug 1994 09:13:53 +0100 (BST) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 331 Recently there has been a discussion on the visualization of vibrational frquencies after QM calculations. One of the responses included reference to two programs that I have not seen, i.e. Xmol and VIBRAM. If you have any information on these programs (and where they are held) could you please contact me. Thanks from Brunel From cletner@remcure.bmb.wright.edu Mon Aug 8 09:30:43 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id JAA06092; Mon, 8 Aug 1994 09:26:54 -0400 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA05778; Mon, 8 Aug 94 09:22:06 -0700 Date: Mon, 8 Aug 1994 08:35:43 -0700 (PDT) From: Charles Letner Subject: Image translation program Summary To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello again, A week ago I asked about programs to do image translation from various graphics formats to high resolution postscript. Here is the summary of the responses as promised. Thanks to everyone that sent a response. Best regards Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu -------------------------------------------- From: Martin Hargreaves Hi, if you have an sgi you have imconv I guess (if not I think you can get it by ftp from sgigate.sgi.com as part of the imgtools package), then there's a thing called tops - man page: TOPS(6D) Silicon Graphics TOPS(6D) NAME tops - Convert an iris image to PostScript SYNOPSIS tops inimage [-l screendensity] [-a screenangle] [-p pixelsperinch] [-x xpixelsperinch] [-y ypixelsperinch] [-b bitsperpixel] [-B ] [-t scaletrim ] [-m maxxinches maxyinches] [-h ] [-o xorg yorg] [-rgb ] [-RGB ] [-cmyk ] [-CMYK ] [-eps ] [-I ] DESCRIPTION tops converts an IRIS image file into Postscript. This program can generate black and white or color PostScript. It can create binary as well as ASCII PostScript. It also can generate encapsulated PostScript with a preview image. I guess you'd have to contact SGI about getting it. It isn't on our system, only the man page.... Regards, Martin. --------------------------- From: David Larson I usually capture my images using the 'snapshot' utility and either import them into 'Showcase' and print them, or use the 'tops' utility to convert the iris rgb images to postscript. I actually like using Showcase better because I can read in a large image and then resize it to fit on a 8.5 x 11" page. Showcase will use all of the data stored in the image when it prints (even though it won't look to good on the screen). To resize the images in Showcase AND maintain the aspect ratio, hold down the key while resizing the image with your mouse. --------------------------------- From: Jussi Eloranta PBMPLUS is a good conversion package. You should be able to find it with archie. jussi ---------------------- From: tj ODonnell Most computer screens are about 100 dpi and so if you are doing a screen dump AND you want your page size to be the same as your monoitor size, you will effectively be getting ~100dpi. If you reduce your image to 1/6th the size on the page compared to the monitor, it will be 600 dpi. So the question is: Are you satisifed with images 1/6 the size? OR Can you produce image files 6 times larger than you now have? of course these will not be viewable on your monitor, except in pieces. If your image is say 600x600 (typical for monitor viewing) the best 600 dpi image will be only 1x1 inch! If you only have 600x600 data, you can only interpolate so far before it starts looking like caca. > there is a file conversion program that will take my image files (TIFF > would be good, though as I said I can output other formats) and output 600 > dpi postscript files? I would like this to be a unix program (I'm using a > SG Indigo II) and viewing capabilities isn't essential for this utility. > As I expect I'm not the first to have this little problem I will send a > summary of the responses. > Your help will be appreciated. On the SGI there are several utilities I use routinely. tops converts an SGI image file (.rgb) to b/w or color postscript and allows you to specify the pixels per inch, or alternatively the max x and y inches. If you are doing b/w on a 600 dpi printer like an AppleWriter or HP laster printer, postscript will be using linescreening to simulate grey levels. In this case BE SURE TO USE -l 80 OR -l 90 INSTEAD OF THE DEFAULT. I think the default is about -l 40 and works well for 300 dpi b/w. On a (dye sublimation) color printer such as the Tektronix, grey levels are accurately printed without linescreens, as are colors. On other color printers, such as ink-jets which dither colors, try -l values with tops. I have not worked extensively with color printers other than dye-subs printers. For black and white images, for example: tops image.rgb -l 90 -p 600 | lp -dhplaser ( for any image size, but output image size on paper will vary ) tops image.rgb -x 2 -y 2 -l 90 | lp -dhplaser (for a 1200x1200 b/w image) where 2 (inches) is 1200(image pixels)/600(pixels/inch). The -l 90 I arrived at by experimentation. 70 to 100 works well. For color images, use the -rgb switch too. For dye sub printers, the -l switch is ineffective, though the -x and -y which determine the effective scale factor greatly influence the quality of the picture, assuming a given image resolution. For example: (assuming a 300 dpi tektronix phaser dye sub printer) tops color.rgb -x 6 -y 6 | lp -dtekphaser (for 1800x1800 color image file) tops color.rgb -x 6 -y 6 | lp -dtekphaser (for 600x600 color image file works OK but scales each pixel 3 times and may look "blocky") The frustrating thing is: if you want true 600dpi resolution you need a 4800x4800 image to get a 8x8 inch output! As for TIFF files, there is a utility to convert TIFF to SGI. try imgcopy (IRIX 5.x only?). There is a fromtiff (to convert TIFF to SGI.RGB) available via anon ftp at sgi.sgi.com (in /sgi/graphics or /pub/graphics or /?/tiff ?). Finally, there is a very nice program on the SG called showcase which can import SGI.RGB files (and TIFF, too?) and output Postscript files. It allows you to re-scale and place the images on the page with text, drawings, etc. There are libraries of public domain file-conversion utilities whose names I forget now. I bet you'll get some responses about these. If not, and you'd like, I'll track them down for you, or try 'archie tiff' Hope this helps. Don't hesitate to ask if you need more help. TJ O'Donnell tj@eecs.uic.edu ------------------------ From: "C.S.RAMAN" What you want is the PBM translation suite. It comes in three different flavors: PBM PBMPLUS NETPBM You can find these at many anon. FTP sites (using ARCHIE). PBM is capable of converting images from one format to numerous others and is extremely useful. Alternatively, you could also try John Christy's ImageMagik available at various anon. FTP sites. You may have to search for some of the utilities that go with it to accomplish your task. Cheers -raman --------------------------------- From: Omar Stradella Depends on what you mean by 91 dpi, that probably really means cells/inch instead of pixels/inch, since your PostScript printer will print at whatever dpi was built or configured for. Let's use as an example your B/W 600 dpi printer, each dot can be only white or black. If you are printing a B/W image (that means no grays at all) such as a molecule represented with circles (balls) and straight lines (sticks) then you can get the full 600 dpi resolution. If you want to print an image with gray levels, the conversion program has to "halftone" the image, halftoning is the process by which continuous-tone colors are approximated by a pattern of pixels that can achieve only a limited number of discrete colors. So now the "points" that form the image are not longer pixels but groups of black and white pixels that combined produce the correct level of gray. So, if your image is 91 cells/inch that is 600/91 = 6 pixels per side or 36 pixels per cell, then 37 levels of gray are possible. Your image looks grainy but you can appreciate the differences of "color". If you convert a rasterized image (like a TIFF file) to PostScript, you'll always have to halftone the image, if you want a finer grain you'll get a smaller range of gray tones. If you want 600 dpi you will get only black and white, no grays at all. In that case I would prefer an image created with PostScript primitives (lines and circles) instead of a rasterized image. Publication quality rasterized images can only be obtained with "publication quality printers", that is 1500 dpi or more, since 1500/6 = 250 cells/inch or 250 gray dots/inch which should look good enough. The same principles apply to color printers. -------------------------------------- From: Dongchul Lim There're a lot of public domain programs which have been written for the very purpose. They are 'PBMPLUS', 'IMAGEMAGIK', 'XV', etc, to just name a few. Among those, what I like most is 'xv' which is available from most anonymous ftp sites. It's pretty small but does all jobs I want to do... -D. Lim ----------------------------- From: Robert Williams You may find that the "pbmplus" package will do what you want. Use archie to find it. If you can't find it, I probably have a path stored here somewhere. Bob Williams ---------------------------- From: Iosif Vaisman I would transfer TIFF file to a PC or Mac, import it to any wordprocessor or graphic program (Word, PowerPoint, Freelance Graphics, etc) and print at desired resolution. --------------------------------- From: Iosif Vaisman I would transfer TIFF file to a PC or Mac, import it to any wordprocessor or graphic program (Word, PowerPoint, Freelance Graphics, etc) and print at desired resolution. ------------------------- From: Johan Landin Hello Chuck, Have you tried the pbmplus package? Included therein are the programs tifftopnm and pnmtops, the first converting from TIFF to pnm (= portable anymap file format) and the second from pnm to PostScript. However, I cannot say anything about the quality of the conversion as I have not tested this conversion myself, just read the manual pages. The pbmplus package is freeware and available on the net. Good luck! /Johan Landin ------------------------------- From: Gernot Katzer Hi Chuck, did you try xv? It's a PD X viewer which supports several graphic formats: GIF, PM, X11 Bitmap, BMP, PS, JPEG, TIFF and some more. Note that not all these formats are accepted as input, but GIF and TIFF are. It should be available via anonymous ftp and easy to install. I use it on a SGI and I am quite happy with it, although I have not tested the PostScript interface excessively. Hope that helps a little, Gernot ------------------------- From: Mr Andrew D Allen We use xv here at Surrey, though i'm not too sure of the resolution of the Postscript output. You could try contacting John Bradley:- John Bradley - bradley@cis.upenn.edu Andy. --------------------------------- From: Bernhard Anton Pabsch High Chuck, have you tried the xv program? You may find it with archie somewhere in the net. On the other hand: Maybe the resolution of your generated pictures is just 91 dpi at highest and no conversion will increase this. Of course, if you can always scale down in size which will increase dpi. So, you might want to save your images in the biggest size and highest resolution initially and then convert and scale down to the desired size. Una volta aperto, conservare in frigo! bap-man ---------------------------- From: "Craig W. Burkhart" Chuck: Since you have an SGI, maybe this will help. In the old IRIX 4.0.5 releases, there was software to perform various RGB image manipulations. Among these were TIFF to RGB (and back again) filters. Also, there was an RGB to PostScript filter in which one of the arguments allowed you to define the output resolution (I believe that 98 dpi is actually the default, not 91, but I may be wrong). These goodies were part of the 4Dgifts software available on the 4.0.5 release. I believe you will need to look for the "giftsfull" (or something) like that) designation when you fire up "inst". If you need more detailed information than this, get back in touch with me and I will give you the EXACT info. I'm doing this off the top of my head {:-). I can tell you that I have used these utilities in the past, and they have really helped me out. The best part is that it is all C source code, so you can play with it if you wish... From ppaneth1@itr1.p.lodz.pl Mon Aug 8 10:31:07 1994 Received: from itr1.p.lodz.pl for ppaneth1@itr1.p.lodz.pl by www.ccl.net (8.6.9/930601.1506) id JAA06528; Mon, 8 Aug 1994 09:49:54 -0400 From: Piotr Paneth To: FR042008@ysub.bitnet, chemistry@ccl.net Subject: CCL:Re:CH3CN and CH3NC X-Mailer: ScoMail 1.0 Date: Mon, 8 Aug 1994 15:41:26 +0200 (MESZ) Message-ID: <9408081541.aa01302@itr1.itr1.p.lodz.pl> We're doing calculations on isotope effects on this stuff (part of it being published). Previously published semi-empirical calculations (J.Phys.Org. Chem. 4,635,1991) yielded N-C-C around 65-67 deg (PM3,MNDO,AM1). References to even earlier calculations are given there. At the moment we have only the following for the transition state: MP2 6-31G N-C-C: 72.3 imaginary freqency: -458.2 cm-1 BLYP 6-31G 69.9 -483.0 BLYP STO-3G 69.9 -496.8 (We're looking for cheep methods of calculating isotope effects and it seems that DFT with even very small basis set works fine). Hope this helps. Piotr ************************************************************************* Piotr Paneth Ph.D., D.Sc. Professor and Vice-chairman Department of Chemistry Technical University of Lodz Zwirki 36, 90-924 Lodz, Poland phone: (+48 42) 31-31-95 fax: (+48 42) 55-29-02 e-mail: ppaneth1@plearn.bitnet or ppaneth1@itr1.p.lodz.pl ************************************************************************* From topper@magnum.cooper.edu Mon Aug 8 10:32:36 1994 Received: from magnum.cooper.edu for topper@magnum.cooper.edu by www.ccl.net (8.6.9/930601.1506) id KAA06776; Mon, 8 Aug 1994 10:11:52 -0400 Received: by magnum.cooper.edu with UUCP id AA01673 (5.65c/IDA-1.4.4); Mon, 8 Aug 1994 10:19:21 -0400 Date: Mon, 8 Aug 1994 10:19:21 -0400 From: Robert_Topper Message-Id: <199408081419.AA01673@magnum.cooper.edu> To: "E. Lewars" , chemistry@ccl.net Subject: Re: CCL:CALCS ON HCN/HNC ISOMERIZATION Content-Length: 1634 With respect to the HCN/HNC isomerization; I can recommend a few useful references as a starting point: J.M. Bowman, B. Gazdy, J.A. Bentley, T.J. Lee, and C.E. Dateo, J. Chem. Phys. 99, 308 (1993); T.J. Lee, C.E. Dateo, B. Gazdy, and J.M. Bowman, J. Phys. Chem. 97, 8937 (1993); J.N. Murrell, S. Carter, and L.O. Halonen, J. Mol. Spec. 93, 307 (1982). In the first of these papers, experimental values are given for the bond lengths and fundamental frequencies for HCN and HNC, taken from several papers by Klemperer/Lehman et. al. . For HCN, the fundamentals are 3311, 713, and 2097 cm^-1; for HNC, " " " 3653, 477, and 2029 cm^-1. The papers by Bowman et.al. and Murrell et.al. seem to be to indicate that when high-level electronic structure methods are used to determine the potential surface and (anharmonic) vibrational perturbation theory [or DVR-DGB variational calculations] are used to calculate the vibrational energy levels, the transition frequencies reproduce experimental values within about 20 cm^-1 or less for both isomers. I hope that this is useful information. best, rqt ************************************************************************ Prof. Robert Q. Topper internet: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 Cooper Square subway: take the N/R to 8th/NYU New York, NY 10003 USA or the 6 to Astor Place ************************************************************************ Thermodynamics forever... From cmanly@mail.nrgn.com Mon Aug 8 12:30:44 1994 Received: from uu9.psi.com for cmanly@mail.nrgn.com by www.ccl.net (8.6.9/930601.1506) id LAA08677; Mon, 8 Aug 1994 11:50:46 -0400 Received: from nrgn.com by uu9.psi.com (5.65b/4.0.071791-PSI/PSINet) via SMTP; id AA09102 for CHEMISTRY@ccl.net; Mon, 8 Aug 94 11:56:51 -0400 Message-Id: <9408081556.AA09102@uu9.psi.com> Date: 8 Aug 1994 11:47:33 -0500 From: "Charles Manly" Subject: Neural Net software To: "chem" Subject: Neural Net software Are there any recommendations for Neural Net software for UNIX (specifically SGI)? I will summarize. Charles Manly cmanly@nrgn.com From SATYAM@vms.cis.pitt.edu Mon Aug 8 13:32:01 1994 Received: from VM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.9/930601.1506) id NAA11929; Mon, 8 Aug 1994 13:10:05 -0400 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.2-14 #4065) id <01HFO1TS1ZRK9S42P2@vms.cis.pitt.edu>; Mon, 8 Aug 1994 13:15:28 EST Date: Mon, 08 Aug 1994 13:15:28 -0500 (EST) Subject: Flourescence Quenching and Ab initio/Semi Empi. QC..Small Mol. To: CHEMISTRY@ccl.net Message-id: <01HFO1TS29EQ9S42P2@vms.cis.pitt.edu> X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, We are interested in knowing if anyone has articles Reviews on Application of Ab initio Theory /Calcns or Semi-empirical QC to explain results of Flourescence Quenching in small molecular systems. If required Summary will be posted Regards Satyam tmQuenching to SaOn From grechtst@pepvax.pepperdine.edu Mon Aug 8 14:30:48 1994 Received: from pepvax.pepperdine.edu for grechtst@pepvax.pepperdine.edu by www.ccl.net (8.6.9/930601.1506) id OAA12977; Mon, 8 Aug 1994 14:00:15 -0400 Received: by pepvax.pepperdine.edu (5.65c/IDA-1.4.4/Pep-5.1) id AA12103 for chemistry@ccl.net; Mon, 8 Aug 1994 11:05:55 -0700 From: Gregory Rechtsteiner Message-Id: <199408081805.AA12103@pepvax.pepperdine.edu> Subject: Scientist Program To: chemistry@ccl.net Date: Mon, 8 Aug 94 11:05:55 PDT X-Mailer: ELM [version 2.3 PL11] Hello: I apologize for this trivial post, especially since an error on my part is the cause. Recently, today(?), someone posted an article about a windows program called "The Scientist" (?) for FTP, etc. Where might I find this program? Thank you very much for your time. Please respond to my pepvax address shown below. Gregory Rechtsteiner -- -------------------------------------------------------------------------------- Gregory A. Rechtsteiner Pepperdine University Research Assistant 24255 PCH # 572 Fax: 310.456.4314 (work) Malibu, CA. 90263 grechtst@pepvax.pepperdine.edu / grechtst@netcom.com -------------------------------------------------------------------------------- From raman@bioc01.uthscsa.edu Mon Aug 8 14:40:00 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id NAA12372; Mon, 8 Aug 1994 13:36:12 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 8 Aug 1994 12:44:35 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04653; Mon, 8 Aug 94 12:42:01 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9408081742.AA04653@bioc01.uthscsa.edu> Subject: Re: CCL:Neural Net software To: cmanly@mail.nrgn.com (Charles Manly) Date: Mon, 8 Aug 1994 12:41:57 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9408081556.AA09102@uu9.psi.com> from "Charles Manly" at Aug 8, 94 11:47:33 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2966 Charles: > Are there any recommendations for Neural Net software for UNIX (specifically > SGI)? The neural network simulator I have used most is called XERION and is available free-of-charge: (a) You can get the source from the anon. FTP site: ai.toronto.edu Look in pub/xerion. (b) There is a mailing list for people using xerion. See the README file for more information. (c) Questions, comments and bugs should be sent to xerion@ai.toronto.edu (d) Here is some additional information on XERION: Xerion is a Neural Network simulator developed and used by the connectionist group at the University of Toronto. This release (Version 3.1) contains libraries of routines for building networks, and graphically displaying them. As well it contains an optimization package which can train nets using several different methods including conjugate gradient. It is written in C and uses the X window system to do the graphics. It is being given away free of charge to Canadian industry and researchers (and anyone else who wants it). It comes with NO warranty. This distribution contains all the libraries used to build the simulators as well as several simulators built using them (Back Propagation, Recurrent Back Propagation, Boltzmann Machine, Mean Field Theory, Free Energy Manipulation, Kohonnen Net, Hard and Soft Competitive Learning). Also included are some sample networks built for the individual simulators. There are man pages for the simulators themselves and for many of the C language routines in the libraries. As well, xerion has online help available once the simulators are started. There is a tutorial on using Xerion in the 'doc' directory. Xerion has been run and (pretty well) tested on the following platforms: SGI Personal Iris and SGI 4d running IRIX 4.0.1 Sun 4 running SunOS 4.1.2 Sun 3 running SunOS 4.0.3 It has been compiled and *minimally* tested on the following platforms: DEC 5000 running ULTRIX DEC Alpha running OSF/1 HP 730 running HP-UX 8.07 (Thanks to Joe Devlin at USC). It has been tested with MIT X11R4 and X11R5 (libraries: Xaw, Xmu, Xt, X11). Xerion will probably run on other machines with some modifications, but we haven't tested it on them and make no guarantees. Hope this helps. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From kallick@gwinn.medc.umn.edu Mon Aug 8 15:30:55 1994 Received: from gwinn.medc.umn.edu for kallick@gwinn.medc.umn.edu by www.ccl.net (8.6.9/930601.1506) id OAA14834; Mon, 8 Aug 1994 14:48:29 -0400 From: Received: by gwinn.medc.umn.edu (911016.SGI/890607.SGI) (for CHEMISTRY@ccl.net) id AA28980; Mon, 8 Aug 94 13:51:32 -0500 Date: Mon, 8 Aug 94 13:51:32 -0500 Message-Id: <9408081851.AA28980@gwinn.medc.umn.edu> To: CHEMISTRY@ccl.net Subject: SANDER Hello All, I'd like to be able to communicate with other NMR people using SANDER. I have no idea how many people are using it, so a reply would be very informative. Deborah Kallick Medicinal Chemistry University of Minnesota 308 Harvard St. S.E. Minneapolis, MN 55455 email: kallick@gwinn.medc.umn.edu From yinona@niva.tau.ac.il Mon Aug 8 15:36:39 1994 Received: from niva.tau.ac.il for yinona@niva.tau.ac.il by www.ccl.net (8.6.9/930601.1506) id PAA16359; Mon, 8 Aug 1994 15:36:39 -0400 Date: Mon, 8 Aug 1994 22:41:53 +0300 (IDT) From: yinon ashkenasy Subject: Re: CCL:Xmol and VIBRAM To: Jeffrey J Gosper Cc: CHEMISTRY@ccl.net In-Reply-To: <6272.9408080813@molnir.brunel.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Xmol is just great to view mol. in a simple fast nit way. you can get it via anonymous ftp from ftp.msc.edu under /pub/xmol get xmol and xmol.[your machine type] about vibram try archie vibram cheers yinon On Mon, 8 Aug 1994, Jeffrey J Gosper wrote: > Recently there has been a discussion on the visualization of vibrational > frquencies after QM calculations. One of the responses included > reference to two programs that I have not seen, i.e. Xmol and VIBRAM. > > > If you have any information on these programs (and where they are held) > could you please contact me. > > Thanks from Brunel > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > From abby@mercury.aichem.arizona.edu Mon Aug 8 16:32:06 1994 Received: from mercury.aichem.arizona.edu for abby@mercury.aichem.arizona.edu by www.ccl.net (8.6.9/930601.1506) id QAA17541; Mon, 8 Aug 1994 16:19:13 -0400 Received: by mercury.aichem.arizona.edu (5.65/DEC-Ultrix/4.3) id AA09530; Mon, 8 Aug 1994 13:25:00 -0700 Date: Mon, 8 Aug 1994 13:15:53 -0700 (MST) From: Abby Parrill Subject: MOPAC restarts To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I currently use MOPAC6.0 on a unix machine. After reading the MOPAC 93 manual information on restarts as well as the information in the regular MOPAC6.0 manual, I am very confused by my inability to restart timed-out mopac jobs. In each case that I have attempted this, the .res file is present in the same directory, and I add the keyword RESTART to the .dat file. Is more than this necessary? The error message that I get by the way is that "NO RESTART FILE EXISTS" __________________________________________________________ Abby Parrill Chemistry Department Artificial Intelligence in Chemistry Laboratory The University of Arizona abby@mercury.aichem.arizona.edu __________________________________________________________ From dwelrod@pwinet.upj.com Mon Aug 8 16:38:27 1994 Received: from pwinet.upj.com for dwelrod@pwinet.upj.com by www.ccl.net (8.6.9/930601.1506) id PAA16788; Mon, 8 Aug 1994 15:45:21 -0400 Received: from cc:Mail by pwinet.upj.com (1.30/SMTPLink) id A11274; Mon, 08 Aug 94 15:50:30 EST Date: Mon, 08 Aug 94 15:50:30 EST From: DWELROD Message-ID: <9408081550.A11274@pwinet.upj.com> To: cmanly@mail.nrgn.com Cc: chemistry@ccl.net Subject: Re: CCL:Neural Net software >Subject: Neural Net software >Are there any recommendations for Neural Net software for UNIX (specifically >SGI)? >Charles Manly cmanly@nrgn.com I have used NeuralWorks Professional II/Plus on a Sun and have been very happy with it. It is also available for SGI, PC, Mac, RS/6000, and HP. It contains most every NN paradigm, has a point & click interface, and they have tools (at an extra cost) that allow you to define your own if you don't like the many that they provide. It is quite expensive, $2000 for PC and $4000 for Sun, etc., but seems quite well done, and I have had good luck getting problems solved by their support people. There are lots of options and modifications you can make within the basic software, so it is good for exploring. NeuralWorks is sold by NeuralWare, Inc., in Pittsburgh (412) 787-8222. A much cheaper ($200?), backprop only package is Nets 3.0, sold by COSMIC, U. of Georgia, Athens, GA. (706) 542-3265 , service@cossack.cosmic.uga.edu. NETS was developed at NASA and is marketed through COSMIC. By the way, COSMIC has a lot of other technical, scientific, and engineering software developed at NASA, but not much chemistry software. NETS comes with compiled code for either PC or Mac, but also has C source code that compiles on just about anything. It has a text-menu driven interface, but having the source code is useful. Dave Elrod ========================================================================== David W. Elrod, Ph.D. Computer-Aided Drug Discovery Computational Chemistry Upjohn Laboratories 301 Henrietta St. Kalamazoo, MI 49007-4940 Phone (616) 385-7772 Fax (616) 385-8488 Internet: dwelrod@upj.com ========================================================================== From elewars@alchemy.chem.utoronto.ca Mon Aug 8 17:32:01 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id RAA18573; Mon, 8 Aug 1994 17:21:05 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id RAA17662 for chemistry@ccl.net; Mon, 8 Aug 1994 17:27:29 -0400 Date: Mon, 8 Aug 1994 17:27:29 -0400 From: "E. Lewars" Message-Id: <199408082127.RAA17662@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Refs to HNC/HCN isomerization Someone recently asked for info or refs to the HNC/HCN reastion. This is briefly discussed, and refs given, in the paper by Sola, Mestres, Carbo and Duran, JACS, 1994 116 (13) 5909-5915; see p 5911, and ref 33 on this p. === From CUNDARIT@MSUVX1.MEMPHIS.EDU Mon Aug 8 19:30:46 1994 Received: from msuvx1.memphis.edu for CUNDARIT@MSUVX1.MEMPHIS.EDU by www.ccl.net (8.6.9/930601.1506) id SAA19236; Mon, 8 Aug 1994 18:40:05 -0400 Received: from MSUVX1.MEMPHIS.EDU by MSUVX1.MEMPHIS.EDU (PMDF V4.3-8 #7188) id <01HFOBBVXQ40A78KCT@MSUVX1.MEMPHIS.EDU>; Mon, 08 Aug 1994 17:46:33 -0500 (CDT) Date: Mon, 08 Aug 1994 17:46:33 -0500 (CDT) From: CUNDARIT@MSUVX1.MEMPHIS.EDU Subject: one bond coupling constants To: chemistry@ccl.net Message-id: <01HFOBBW1QSIA78KCT@MSUVX1.MEMPHIS.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, A collaborator of ours asked if it is possible to calculate 1J(PH), i.e. an NMR one bond coupling constant, from a standard Hartree-Fock calc (accuracy is another issue). Since I did not know, I thought I would put this out on the net. If anyone has any software/idea abut how to do this, it would be greatly appreciated. Any empirical schemes for estimating such a parameter (e.g., a correlation with 1J and the PH strecthing frequency, Mulliken bond overlap population, bond length, etc.) would also be welcome, if not more so. Tom ------------------------------------------------------------------------------ Thomas R. Cundari Address until the end of August Asst. Professor of Chemistry Tom Cundari Computational Inorganic Chemistry Lab Visiting Scientist University of Memphis CST-3, C346 Memphis, TN 38152 Los Alamos National Lab phone: 901-678-2629 Los Alamos, NM 87545 fax: 901-678-3447 phone: 505-665-8014 e-mail: cundarit@memstvx1.memst.edu fax: 505-665-3688 http://www.memst.edu/chemistry/umchem.html e-mail: same as always -------------------------------------------------------------------------------