From chemistry-request@ccl.net Fri Apr 10 01:09:28 1992 Date: Fri, 10 Apr 92 13:12:23 EST From: Dave Winkler (Dr.) Subject: Metabolism prediction software To: chminf-l@iubvm.ucs.indiana.EDU, chemistry@ccl.net Status: R Dear Netters, I am trying to find software packages which predict metabolism of drugs or other xenobiotics in animals, plants or insects. Todd Wipke was working on this in the early 80s and I believe there is a company called CompuDrug (based on work of Ferenc Darvas?) who may sell the software. Has anyone used this type of software, can they give me names, fax or email adresses, and tell me how well it works? I would be keen to hear from anyone working in the field as well. I am happy to summarize responses for the net. Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. From chemistry-request@ccl.net Fri Apr 10 04:15:03 1992 Date: 10 Apr 92 08:42:27+0100 From: SBPM Marc GINGOLD Subject: Re: Graphics packages To: chemistry@ccl.net, srahman@pellns.alleg.EDU Status: R >From anonymous ftp: gnuplot (linked to emacs, TeX too) khoros (specially for images) many plot... for PC,Amiga,Max (and cc3/cc4) See archie to get the addresses! From chemistry-request@ccl.net Fri Apr 10 11:42:18 1992 Date: Fri, 10 Apr 1992 09:45:24 -0400 From: jkl@ccl.net Subject: Re: Graphics packages To: chemistry@ccl.net Status: R Forwarding to the list: ---------- Begin Forwarded Message ---------- = From rupley!local@cs.arizona.edu Thu Apr 9 19:55:08 1992 = Date: Thu, 9 Apr 92 23:55:55 GMT = From: rupley!local@cs.arizona.edu = To: arizona!ccl.net!chemistry-request@cs.arizona.edu = Subject: Re: Graphics packages = Cc: rupley!local@cs.arizona.edu | I would like to get some feedback on experience people have | made in using packages available for visualization of scientific | data. We tried several, but were not particularly happy with any of | them. In particular, how does the package from NCAR(?) compare with | other packages such as IDL and PV-WAVE? (We were not able to look at | the NCAR(?) graphics because they do not ship a demo copy, you must | buy one for about $700.) WAVEFRONT is too expensive. Is AVS an | overkill for visualization of scientific data? What about apE? Thanks ^^^^^^^^^^^^^^^ | in advance. For multivariate data, as distinguished from the results of simulations, perhaps you should try xgobi, software from ATT bellcore, available by ftp (i.e., distributed freely) from lib.stat.cmu.edu, login as statlib, mget xgobi* from ~ftp/general. It is a _very_ nice package for viewing data and finding patterns and relationships. It has an S interface, which makes it even more attractive. Regards, John Rupley Biochemistry rupley@cs.arizona.edu ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Fri Apr 10 12:07:46 1992 Date: Fri, 10 Apr 1992 09:47:56 -0400 From: jkl@ccl.net Subject: Re: Graphics pac To: chemistry@ccl.net Status: R Forwarding to the list: ---------- Begin Forwarded Message ---------- = From rupley!local@cs.arizona.edu Fri Apr 10 02:14:29 1992 = Date: Fri, 10 Apr 92 06:15:19 GMT = From: rupley!local@cs.arizona.edu = Message-Id: <9204100615.AA20211@rupley> = To: arizona!ccl.net!chemistry-request@cs.arizona.edu = Subject: Re: Graphics packages = Cc: rupley!local@cs.arizona.edu Another comment, as followup on a recommendation of xgobi for viewing data interactively (3-d rotation, scatterplot cycling, data brushing, etc)... If one wants to plot data, try S, available for small or medium bucks >from stat sci as executables, for machines from PC's up, or as source for more bucks from USL. S has a sophisticated set of routines for generating plots, labels, curves, etc., to taste. Postscript and other drivers for hard copy, X for viewing. Viewgraphs. This in addition to the real use of S: for statistical analysis, matrix manipulation, data reduction, etc. John Rupley Biochemistry rupley@cs.arizona.edu ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Fri Apr 10 12:33:06 1992 Date: Fri, 10 Apr 92 08:08:59 EDT From: Shaun Black Subject: Plotting of Scientific Data To: chemistry@ccl.net Status: R Our laboratory generates a variety of spectral, computational, and chromatographic data. We have found that the SlidewritePlus package (DOS, PC) meets most of our needs. Data from ASCII files can be imported readily, graphs are generated in a quick, interactive fashion, and the software will produce output on a wide variety of devices or can make two formats of PostScript file. We typically produce color PostScript images of our plots and send them to one of a variety of PostScript printers either directly or over the network. One feature that we have found quite useful is the ability to curve-fit data by automatic or user-imput functions; splines, polynomials, and exponentials are examples of built-in functions and sigmoids are examples of functions that we have input and used. Another nice capability is the ability to perform mathematics on whole data arrays or segments thereof; arrays can be added, subtracted, etc. to one another or can be transformed by any mathematical expression of your choice. The overall process is general, easy, and quick. For the record, I have no affilitation with the software vendor, but am simply a satisfied user. If you're interested in the address, further information, or a sample PostScript file, let me know. I'd be more than glad to help. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= - Shaun D. Black, PhD | Bitnet: black@ohstphrm.bitnet - = Ohio State University | Internet: black@ohstphrm.pharmacy.ohio-state.edu = - College of Pharmacy | Phone: (614) 292-3925 - = 500 West 12th Avenue | FAX: (614) 292-2435 = - Columbus, OH 43210-1291 | :-) (...Start every day with a smile...) - =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Fri Apr 10 15:33:13 1992 Date: Fri, 10 Apr 92 12:37 CDT From: PAVAN@aardvark.ucs.uoknor.EDU Subject: gnuplot To: chemistry@ccl.net Status: R Hai Can somebody tell me how to get the gnuplot software? thanks for the help pavan pavan@aardvark.ucs.uoknor.edu pavan@uokucsvx From chemistry-request@ccl.net Fri Apr 10 19:07:24 1992 Date: Fri, 10 Apr 92 14:45:18 -0700 From: yee@gold.cchem.berkeley.EDU (Raymond Yee) Subject: calculating S(k) from g(r) To: chemistry@ccl.net Status: R Hello, I would appreciate some help on how to calculate S(k) from g(r) (the radial distribution function) on a computer. What is a good algorithm to do the Fourier sine transform? Is the FFT a good way to calculate structure factors from g(r)? Do you do smoothing of any sort on the g(r) (or splining)? Do you try to extrapolate g(r) to larger r's to get better results? Allen & Tildesley mention a method by Lado and one by Filon -- have any of you tried these algorithms? Finally, how about calculating S(k) directly (during a simulation run) -- is that a good way? Thanks in advance, Raymond Yee From chemistry-request@ccl.net Fri Apr 10 22:44:33 1992 Date: Fri, 10 Apr 92 21:29:20 -0400 From: neal@serj.polymer.uakron.EDU (Neal Neuburger) Subject: gnuplot To: chemistry@ccl.net Status: R To obtain gnuplot in: NORTH AMERICA: Anonymous ftp to dartmouth.edu (129.170.16.4) Fetch pub/gnuplot/gnuplot3.0.tar.Z in binary mode. Users without ftp capability can obtain it through a mail ftp server. Send a mail message saying 'help' to BITFTP@pucc.princeton.edu for instructions. For a uuencoded copy of the gnuplot sources (compressed tar file), send this message to BITFTP@pucc.princeton.edu: FTP DARTMOUTH.EDU UUENCODE USER ANONYMOUS CD pub/gnuplot BINARY GET gnuplot3.0.tar.Z QUIT Neal Neuburger