From jolanala@amu.edu.pl Fri May 29 09:46:46 1998 Received: from main.amu.edu.pl (root@main.amu.edu.pl [150.254.65.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA09012 Fri, 29 May 1998 09:43:45 -0400 (EDT) Received: from main.amu.edu.pl (jolanala@main.amu.edu.pl [150.254.65.2]) by main.amu.edu.pl (8.8.8/8.8.8) with SMTP id PAA06971 for ; Fri, 29 May 1998 15:42:47 +0200 (MET DST) Date: Fri, 29 May 1998 15:42:47 +0200 (MET DST) From: Jolanta Latosinska To: CHEMISTRY@www.ccl.net Subject: request Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Does anybody know or have got the pdb files as well as log p or the other biological activity data for the following steroid compounds: ethisterone, norethisterone, deoxycorticosterone,testosterone, progesterone, estradiol, estriol, estrone. Colud you send your answer to e-mail: jolanala@amu.edu.pl. Best regards, Jolanta Latosinska From mildred@houdini.tds-tds.com Fri May 29 15:50:46 1998 Received: from houdini.tds-tds.com ([207.99.16.200]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA11068 Fri, 29 May 1998 15:50:45 -0400 (EDT) Received: from houdini.tds-tds.com ([207.99.16.200]) by houdini.tds-tds.com (Netscape Mail Server v2.0) with SMTP id AAA4486; Fri, 29 May 1998 15:13:41 -0500 Date: Fri, 29 May 1998 15:13:41 -0400 (EDT) From: "Mildred R. Green PhD" To: Jolanta Latosinska cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:request In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII TDS can provide experimental log P data for compounds like the ones you list. We also are a source for substituent parameters which are used for calculating biological activity. Please contact me if you wish to obtain further information. Mildred Green ------------------------------------------------------------------------------ Technical Database Services, Inc (TDS) EMAIL: mrgreen@tds-tds.com Phone: 212 245 0044 FAX: 212 247 0587 WEBSITE: http://www.tds-tds.com ------------------------------------------------------------------------------ On Fri, 29 May 1998, Jolanta Latosinska wrote: > Dear all, > Does anybody know or have got the pdb files as well as log p or the > other biological activity data for the following steroid > compounds: > ethisterone, norethisterone, deoxycorticosterone,testosterone, > progesterone, estradiol, estriol, estrone. > Colud you send your answer to e-mail: jolanala@amu.edu.pl. > Best regards, > Jolanta Latosinska > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jolanala@amu.edu.pl > -- Original Sender From: Address: jolanala@amu.edu.pl > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From daizadeh@kappa.ucdavis.edu Fri May 29 17:10:40 1998 Received: from kappa.ucdavis.edu (kappa.ucdavis.edu [128.120.7.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA11551 Fri, 29 May 1998 17:10:38 -0400 (EDT) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id OAA12836 for chemistry@www.ccl.net; Fri, 29 May 1998 14:10:55 -0700 From: "Iraj Daizadeh" Message-Id: <9805291410.ZM12834@kappa.ucdavis.edu> Date: Fri, 29 May 1998 14:10:55 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Summary: Surface! Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello and thank you for your responses. This is what I have tried so far (or thought about): 1. gnuplot (freeware): splot "filename" w l set noparametric replot splot "filename" w p 2. plotmtv (freeware): $data=curve3d % meshplot = on % hiddenline = off % spline = 100 % yflip = on % xflip = on Similar result as above! Just a jumble of misconnected data points. 3. scilab (freeware): I have simply not tried it. This program is similar to matlab. In fact, I heard that the makers of matlab also made scilab (but I do not know this for sure). 4. Other ideas that I would like to try: vis5d: http://www.ssec.wisc.edu/~billh/vis5d.html Vu: http://www.cerca.umontreal.ca/vu/Welcome_eng.html tecate: http://www.sdsc.edu/projects/Tecate/tecate.html tipsy: http://www-hpcc.astro.washington.edu/tools/TIPSY/ scian: http://www.scri.fsu.edu/~lyons/scian/ All of the above programs are freely available. Thanks again. Iraj. My original inquiry was: ------------------------------------------------------- ------------------------------------------------------- Hello. I have a file that contains x,y, and z of a three-dimensional surface and would like to display this. What programs are easy and fast to do that is capable to perform this task? xmgr is for 2d and plotmtv has 2d and 3d capabilities including vectors but cannot build a surface in 3d unless one has already an insight into what the surface should look like. Are there any free programs that are of this calibar (publication ready output)? I will summarize the results as is typical. Thanks in advance. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Responses: Try gnuplot. You can find it in most GNU website. ------------------------------------------------------------------ Hongyu Zhang, Ph.D. | Tel: (301) 738-6117 (w) ^/..\^ CARB, University of Maryland | (301) 987-0179 (h) -m( 00 )m- 9600 Gudelsky Drive | Fax: (301) 738-6255 Rockville, Maryland 20850 | Email: hyzhang@carb.nist.gov URL: http://indigo5.carb.nist.gov/~hyzhang ------------------------------------------------------------------ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx helo, there is old good program (unfortunately, for windows) called winsurf. very fast: 1)make grid from xyz file, 2) plot a surface from grid ___________________________________________________ | Alexander Kulak, | Institute for Physical Chemical Problems | activity area: solid state computational chemistry xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I think gnuplot does. you can get it from the net. Steven xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hi! There are 2 possibilities for your case: 1) z = f(x,y), i.e. what you really want is to display the graph of a 2-dimensional function. Many programs can do that, including gnuplot, MS Excel, etc. 2) you simply have a unconstrained set of points (x_i,y_i,z_i) in 3d-space. Then you will first need to apply an algorithm that finds - let's say - the enclosing surface of this set of points. Triangulation is such an algorithm and it is implemented in the more advanced visualization packages like AVS, Explorer, ... hope this helps, gerald ---------------------------------------------------------------------- Gerald Loeffler - Bioinformatics Scientist Boehringer Ingelheim R&D Vienna, Molecular Biology Department Email: Gerald.Loeffler@vienna.at Phone: +43 676 3289588 (and +43 1 80105 634) Fax: +43 1 80105 683 Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I don't know of the cost but we use Stanford Graphics here which plot beautiful colour 3D graphs from just the data you describe It is published by Visual Numerics Inc. www.vni.com but I can't find anything on their web site. The following has more info though http://www.greymatter.co.uk/gmWEB/Nodes/NODE0496.HTM Hope this helps Carl > I have a file that contains x,y, and z > of a three-dimensional surface and would like > to display this. -- --------------------------------------------------------------- |E-mail for life: carl.windsor@bigfoot.com | --------------------------------------------------------------- |Carl Mark Windsor - Ph.D Student in Computational Chemistry, | | University of Manchester, | | Oxford Road, | | Manchester. | --------------------------------------------------------------- |"Do...or do not, there is no try" Yoda, Jedi Master | --------------------------------------------------------------- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Encoded with "quoted-printable" ] : Iraj, if you aren't able to state any constraints about your 3d-data to my experience it is the best idea to compute an alpha-shape, e.g. with the software made available by Edelsbrunner and coworkers (a web-site should exist with possibilities for downloads). I'm interested in your summary. Best regards, Friedrich ------------------------------------------------------------------ Dr. Friedrich Ackermann Dade Behring Marburg GmbH Instrumentation / Software Am Kronberger Hang 3 D-65824 Schwalbach Germany Phone: +49 (6196) 806-440 (-300) Fax: +49 (6196) 806-320 mailto: ackermann@behring-instruments.de ------------------------------------------------------------------ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hello. I'm interested too. (excuse for my Engish) If anybody would be so kind that he helps you, I'll be grateful to you for your report. Alex Rylov. (alexr@abbyy.ru) P.S. I know the program of Golden Software Inc. - SURFER for Windows v. 5.01. This vertion works under Windows 3.1, Win'95, WinNT. I can give you this version, if it's necessary. But this program not take into account, for instance, that coordinates can be cyclic (as torsion angle). That's why SURFER can distort the surface. I'm interested in a program that also allows to cut off the interpolation before triangulation. Alex Rylov xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx GRASS can only plot surfaces where z=f(x,y), in other words, there is one and only one z for each x,y such as terrain. It sounds like you have a more complex surface so the software would need to derive some kind of connectivity information. If the 3d points also contain values such as concentration of chemicals, you may derive isosurfaces of concentration, which could result in a tube-like structure, or if you have surface normals at the points there might be software that can derive an implied surface (but not in GRASS). We have 3d modules in our version of GRASS that can plot isosurfaces, but this code has not been released to the public. There are a variety of visualization packages that can do the same thing. Depending on the density of your points, you might also be able to get a rough isosurface by using spatial interpolation, starting with only values at your points and zeros elsewhere. Then with some reclassification of the resulting interpolated 3Dgrid, you might get a tube-like isosurface. There are probably more advanced algorithms for finding such surfaces, but we have not implemented any. For visualization, you might start with simply making a scatter plot of the 3d points, if you haven't already. hope this helps - Bill xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx gnuplot may be able to do what you need. It has been a while since I used it, but I know it will give a decent surface. I believe it is freeware, but I don't know the website for it. Best, Ken _____________________________________________________________________ /| | /| Kenneth E. Lind, Graduate Student | /| Department of Medicinal Chemistry, University of Minnesota | /| | /| phone: (612) 626-3551 fax: (612) 626-4429 | /| e-mail: lind@vwl.medc.umn.edu url: http://chet.medc.umn.edu/~lind | /|_____________________________________________________________________| / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Ihis could be done with with the public domain ray-tracing program POV-Ray; for more info see http://www.povray.org -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hi, I have found that MS Excell works fine to do 3D graphs and to plot surfaces. The only problem is that you need the data to be arranged in a matrix form: x1 x2 x3 ... y1 z11 z12 z13 ... y2 z21 z22 z23 .. ... If you have x,y,z then you can do some macro to have the data in the above form. Hope this helps, Edgar E. Arcia Grad. Student Chemistry University of Montana ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. <_^_> arcia@mail.mssl.uswest.net (.,.) earcia@selway.umt.edu ____ooO Ooo________________________________ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Try GnuPlot. - Jack > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Jack A. Smith || > Union Carbide || Phone: (304) 747-5797 > Catalyst Skill Center || FAX: (304) 747-4672 > P.O. Box 8361 || > S. Charleston, WV 25303 || smithja@ucarb.com > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu