From chemistry-request@www.ccl.net Wed Oct 21 02:06:56 1998 Received: from hestia.its.deakin.edu.au (hestia.its.deakin.edu.au [128.184.136.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA12179 Wed, 21 Oct 1998 02:06:53 -0400 (EDT) Received: from [128.184.88.60] (ara10.bcs.deakin.edu.au [128.184.88.60]) by hestia.its.deakin.edu.au (8.8.8/8.8.8) with ESMTP id QAA27316; Wed, 21 Oct 1998 16:06:28 +1000 (EST) X-Sender: lim@128.184.136.2 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Oct 1998 16:04:46 +1000 To: chemistry@www.ccl.net From: "Kieran F Lim (Lim Pak Kwan)" Subject: a good graphing analysis package? Cc: molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, chemistry@uniserve.edu.au, physics@uniserve.edu.au We are seeking a dual platform (Mac and PC) graphing and analysis package. This should have the ability to do - curve fitting (including user-defined functions) - 2-d and 3-d plots - plots suitable for insertion into both hardcopy and electronic documents (not everthing does the latter well!) Can you recommend a package based on your experiences? Sorry if you get multiple copies of this message. Thank you, Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@www.ccl.net Wed Oct 21 02:30:20 1998 Received: from wotho.pd.uwa.edu.au (root@wotho.pd.uwa.edu.au [130.95.156.81]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA15555 Wed, 21 Oct 1998 02:30:17 -0400 (EDT) Received: from [130.95.156.21] (fock [130.95.156.21]) by wotho.pd.uwa.edu.au (8.9.1/8.9.1/Debian/GNU) with ESMTP id OAA18315; Wed, 21 Oct 1998 14:28:52 +0800 Message-Id: In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Oct 1998 14:31:49 +0800 To: Kieran Lim From: Paul Abbott Subject: Re: a good graphing analysis package? Cc: chemistry@uniserve.edu.au, chemistry@www.ccl.net, molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, John Brookes At 2:04 PM +0800 21/10/98, Kieran F Lim (Lim Pak Kwan) wrote: >We are seeking a dual platform (Mac and PC) graphing and analysis >package. This should have the ability to do > - curve fitting (including user-defined functions) > - 2-d and 3-d plots > - plots suitable for insertion into both hardcopy and electronic > documents (not everthing does the latter well!) > >Can you recommend a package based on your experiences? Mathematica does all of these things well (and more). You can find out more about Mathematica at http://www.wolfram.com Some examples of chemistry applications of Mathematica can be found at http://www.wolfram.com/engineering/users.html and some research papers in Chemistry and Chemical Engineering that have used Mathematica are listed at http://www.wolfram.com/papers/chem.html In addition, I find it to be an excellent teaching tool. Hope this helps. Cheers, Paul ____________________________________________________________________ Paul Abbott Phone: +61-8-9380-2734 Department of Physics Fax: +61-8-9380-1014 The University of Western Australia Nedlands WA 6907 mailto:paul@physics.uwa.edu.au AUSTRALIA http://www.physics.uwa.edu.au/~paul God IS a weakly left-handed dice player ____________________________________________________________________ From chemistry-request@www.ccl.net Wed Oct 21 03:33:21 1998 Received: from fg702-6.abct.polyu.edu.hk (fg702-6.abct.polyu.edu.hk [158.132.74.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA25823 Wed, 21 Oct 1998 03:33:19 -0400 (EDT) Received: from danspc (dannt.polyu.edu.hk [158.132.31.49]) by fg702-6.abct.polyu.edu.hk (8.8.8/8.8.8) with SMTP id PAA07371 for ; Wed, 21 Oct 1998 15:34:02 +0900 (HKST) Message-Id: <3.0.2.32.19981021153915.00990d58@fg702-6.abct.polyu.edu.hk> X-Sender: dkwmok@fg702-6.abct.polyu.edu.hk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Wed, 21 Oct 1998 15:39:15 To: CHEMISTRY@www.ccl.net From: Daniel Mok Subject: G:Options in Potential Scan Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, I wonder is there any keyword to control the output precision of the summary of a Gaussian potential scan job. The summary gives energy in five decimal places only and I would like the table with more significant figures. Thanks Daniel Hong Kong Polytechnic University From chemistry-request@www.ccl.net Wed Oct 21 05:16:49 1998 Received: from phy.hw.ac.uk (root@innpin.phy.hw.ac.uk [137.195.28.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA11940 Wed, 21 Oct 1998 05:16:48 -0400 (EDT) Received: from optfs1.phy.hw.ac.uk (optfs1 [137.195.28.77]) by phy.hw.ac.uk (8.8.8/8.8.8) with ESMTP id KAA03475; Wed, 21 Oct 1998 10:16:27 +0100 (BST) Received: from OPTFS1/SpoolDir by optfs1.phy.hw.ac.uk (Mercury 1.40); 21 Oct 98 10:16:31 GMT +0100 Received: from SpoolDir by OPTFS1 (Mercury 1.40); 21 Oct 98 10:16:09 GMT +0100 From: "ROBERT R J MAIER" Organization: Heriot-Watt Physics Dept To: chemistry@www.ccl.net, "Kieran F Lim (Lim Pak Kwan)" Date: Wed, 21 Oct 1998 10:16:04 GMT +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: a good graphing analysis package? CC: molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, chemistry@uniserve.edu.au, physics@uniserve.edu.au Priority: normal In-reply-to: Message-ID: <13A8D47B55@optfs1.phy.hw.ac.uk> MICROCAL's ORIGIN Versions 4 and 5 should fit all your requirements http://www.microcal.com Robert Date: Wed, 21 Oct 1998 16:04:46 +1000 Subject: a good graphing analysis package? From: "Kieran F Lim (Lim Pak Kwan)" To: chemistry@www.ccl.net Cc: molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, chemistry@uniserve.edu.au, physics@uniserve.edu.au Reply-to: "Kieran F Lim (Lim Pak Kwan)" We are seeking a dual platform (Mac and PC) graphing and analysis package. This should have the ability to do - curve fitting (including user-defined functions) - 2-d and 3-d plots - plots suitable for insertion into both hardcopy and electronic documents (not everthing does the latter well!) Can you recommend a package based on your experiences? Sorry if you get multiple copies of this message. Thank you, Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim Robert Maier; Dipl.Ing.; Research Associate Optoelectronics and Laser Engineering Group Department of Physics; Heriot-Watt University Edinburgh EH14 4AS; Scotland; UK Tel: +44(0131)4513084; Fax: +44(0131)4513088 email: r.r.j.maier@hw.ac.uk From chemistry-request@www.ccl.net Wed Oct 21 08:36:30 1998 Received: from granite.sentex.net (granite.sentex.ca [199.212.134.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA13646 Wed, 21 Oct 1998 08:36:29 -0400 (EDT) Received: from pppuser.uoguelph.ca (p43.argon.sentex.ca [209.112.4.236]) by granite.sentex.net (8.8.6/8.6.9) with SMTP id IAA19047; Wed, 21 Oct 1998 08:36:24 -0400 (EDT) Message-Id: <199810211236.IAA19047@granite.sentex.net> X-Sender: mathtrek@mathtrek.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 Date: Wed, 21 Oct 1998 08:35:10 -0400 To: chemistry@www.ccl.net From: "W. R. Smith" Subject: Re: CCL:a good graphing analysis package? Cc: molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, chemistry@uniserve.edu.au, physics@uniserve.edu.au In-Reply-To: <13A8D47B55@optfs1.phy.hw.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" >Date: Wed, 21 Oct 1998 16:04:46 +1000 >Subject: a good graphing analysis package? >From: "Kieran F Lim (Lim Pak Kwan)" >To: chemistry@www.ccl.net >Cc: molecular-dynamics-news@mailbase.ac.uk, spectroscopy-group@mailbase.ac.uk, > chemistry@uniserve.edu.au, physics@uniserve.edu.au >Reply-to: "Kieran F Lim (Lim Pak Kwan)" > >We are seeking a dual platform (Mac and PC) graphing and analysis >package. This should have the ability to do > - curve fitting (including user-defined functions) > - 2-d and 3-d plots > - plots suitable for insertion into both hardcopy and electronic > documents (not everthing does the latter well!) > >Can you recommend a package based on your experiences? > >Sorry if you get multiple copies of this message. SigmaPlot is the primier such package for a PC - I don't know if a Mac version exists. See the web site http://www.spss.com/software/science/sigmaplot/ -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From chemistry-request@www.ccl.net Wed Oct 21 09:37:15 1998 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA23408 Wed, 21 Oct 1998 09:37:14 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA28944 (5.65c/IDA-1.4.4 for ); Wed, 21 Oct 1998 09:34:32 -0400 Received: by zeus.cooper.edu id AA16420 (5.67b/IDA-1.5 for CHEMISTRY@www.ccl.net); Wed, 21 Oct 1998 09:36:15 -0400 From: TOPPER ROBERT Message-Id: <199810211336.AA16420@zeus.cooper.edu> Subject: CCL:a good graphing analysis package? To: CHEMISTRY@www.ccl.net Date: Wed, 21 Oct 1998 09:36:14 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit For all plots and curve fits two-dimensional, nothing beats KaleidaGraph IMHO. It is an incredibly fast, robust program available for Macs and PCs. Moreover it is easy to use - I have shown freshman students how to make fairly complex plots in minutes. It is trivial to add error bars (x and/or y axis) to some or all of the points of a data set. You can easily define your own curves for plotting to compare with your data, use their pre-set fitting routines (which are quite robust) or define your own function for fitting. The graphics it produces are camera-ready when printed on a laser printer. In short: I have been using KG for many years and highly recommend it. It's available from Synergy Software, and is CHEAP with an academic discount. (www.synergy.com; (610) 779-0522 is the number (unless it's changed since last time I called). KaleidaGraph will run just fine on a Mac Classic (I do this sometimes in a pinch) and is screamingly fast on even a minimal PowerMac. However, it (sadly) cannot do 2D plots. For such things, I typically use Mathematica, MathCAD or a similar package (which will not run on some of my older 000-040 Macs). Both are available for PC and Mac platforms. Mathematica can do many of the 2D plotting things one would need to do, as can MathCad. However, I doubt whether those packages can be easily used to add error bars to data points (although I'm sure someone out there will tell me if I'm wrong. :-) ), so I can't recommend them as your sole solution or 2D and 3D plotting (since I always include error bars in my calculations). SigmaPlot can do all you want, but last I heard it was not available on both Mac and PC platforms. You might consider running it on a G3 PowerMac using SoftWindows or some similar product - the performance should be decent and one program will do everything you need. ***************************************************************************** Robert Q. Topper email: topper@cooper.edu Asst. Professor of Chemistry phone: (212) 353-4341 The Cooper Union fax: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 and you're there! http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** The Cooper Union for the Advancement of Science and Art is a tuition-free college in Greenwich Village, at Cooper Square and Astor Place. ***************************************************************************** Forwarded message: > Date: Wed, 21 Oct 1998 16:04:46 +1000 > To: chemistry@www.ccl.net > From: "Kieran F Lim (Lim Pak Kwan)" > Subject: CCL:a good graphing analysis package? > > We are seeking a dual platform (Mac and PC) graphing and analysis > package. This should have the ability to do > - curve fitting (including user-defined functions) > - 2-d and 3-d plots > - plots suitable for insertion into both hardcopy and electronic > documents (not everthing does the latter well!) > > Can you recommend a package based on your experiences? > > Sorry if you get multiple copies of this message. > > Thank you, > > Kieran > > ------------------------------------------------------------ > Dr Kieran F Lim Biol. and Chemical Sciences > (Lim Pak Kwan) Deakin University > ph: + [61] (3) 5227-2146 Geelong VIC 3217 > fax: + [61] (3) 5227-1040 AUSTRALIA > mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim > From chemistry-request@www.ccl.net Wed Oct 21 10:45:38 1998 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA05127 Wed, 21 Oct 1998 10:45:37 -0400 (EDT) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA13852; Wed, 21 Oct 1998 15:42:10 +0100 Received: from munch.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA22202; Wed, 21 Oct 1998 15:45:28 +0100 Date: Wed, 21 Oct 1998 16:45:28 +0200 (MET DST) From: David van der Spoel X-Sender: spoel@munch To: TOPPER ROBERT Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:a good graphing analysis package? In-Reply-To: <199810211336.AA16420@zeus.cooper.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII After this bombardment of e-mails on comercial graphics packages, I would like to suggest using xmgr for your 2D graphics. It is easy to use, and includes non-linear curve fitting. It is free software and runs on any UNIX implementation including Linux, and therefore will run on your PC and Mac machines. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Wed Oct 21 14:57:34 1998 Received: from sp2n17.missouri.edu (sp2n17-a.missouri.edu [128.206.3.17]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA08258 Wed, 21 Oct 1998 14:57:32 -0400 (EDT) Received: from sp2n23-t.missouri.edu (sp2n23.missouri.edu [128.206.2.84]) by sp2n17.missouri.edu (8.9.0/8.9.0) with ESMTP id NAA57134 for ; Wed, 21 Oct 1998 13:57:31 -0500 Received: from localhost (chemtw@localhost) by sp2n23-t.missouri.edu (8.9.0/8.9.0) with SMTP id NAA98154 for ; Wed, 21 Oct 1998 13:57:31 -0500 X-Authentication-Warning: sp2n23-t.missouri.edu: chemtw owned process doing -bs Date: Wed, 21 Oct 1998 13:57:30 -0500 (CDT) From: Troy Wymore X-Sender: chemtw@sp2n23-t.missouri.edu To: chemistry@www.ccl.net Subject: CHARMM/Density from COM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to calculate the density of specific atoms from the center-of-mass of a micelle along a trajectory. The only way I know that will work is to orient the mass of the micelle to the origin and analyze the density from that point. The trajectory is quite long and so orienting all those frames may take a lot of time and then the water molecules would be out of position (?) and I would like to analyze the water density from the micelle COM too. Is there an easier way to do this? Any help would be much appreciated. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** From chemistry-request@www.ccl.net Tue Oct 20 11:15:13 1998 Received: from leona.harvard.edu (daizadeh@leona.harvard.edu [128.103.96.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA09123; Tue, 20 Oct 1998 11:15:12 -0400 (EDT) Received: from localhost (daizadeh@localhost) by leona.harvard.edu (8.8.7/8.8.7) with SMTP id LAA20399; Tue, 20 Oct 1998 11:15:49 -0400 Date: Tue, 20 Oct 1998 11:15:49 -0400 (EDT) From: Iraj Daizadeh To: medvedev@sigma.ucdavis.edu, guo@indigo.ucdavis.edu, antony@indigo.ucdavis.edu, fink@indigo.ucdavis.edu, gilbert@nucleus.harvard.edu, chemistry@www.ccl.net, chemistry-request@www.ccl.net, stuchebr@indigo.ucdavis.edu cc: Iraj Daizadeh Subject: Summary:Protein Visualization/Protein Manipulation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues: This summary is organized as follows: I) Original Question posed to the CCL. II) In Brief, A table enumerating the software products: Software Name Platform(s) WebSite III) Full Summaries Please read the full summaries before proceding to the WebSite: most programs satisfy the question posed, a couple do not (but they come very close!). Thank you for your responses to my question, I hope that this summary will be of use to many of you in the near future. Sincerely, Iraj. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I) Original Query: Hello. I am in search of a program that is able to display multiple protein structures at the same time (viz. on the screen) and is able to manipulate them independently. The resolution of the structures displayed may be primitive. I know that RasMol is able to do this for up to five molecules. Any information concerning other programs preferably free would be appreciated. A summary will be posted on the CCL as is customary. Thank you. Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Chemistry and Chemical Biology 12 Oxford Street, Box #35 Cambridge, MA 02138-2902 Phone: 617-495-2654 Fax: 617-495-1823 email: daizadeh@lhasa.harvard.edu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx II) Software Name Platform(s) WebSite MOLVIEW MAC/soon Windows www.bio.cam.ac.uk/proj/teaching/ virology/MolView/MolView.html GOPENMOL DEC,PC/LINUX,SGI laaksonen.csc.fi/gopenmol/gopenmol.html SWISS-PDB Mac,PC,SGI(Soon) expasy.hcuge.ch/spdbv/mainpage.html MOLDEN SGI,SUN,DEC,CRAY,IBM, www.caos.kun.nl/~schaft/molden/molden.html LINUX,HP,VAX,OpenVMS, Windows/NT,Windows95,OS2 MMTK ** LINUX/UNIX starship.skyport.net/crew/hinsen/mmtk.html MAC-molecule2/ Name Says it All www.molvent.com/ pc-molecule2 MOLMOL UNIX,WindowsNT/95 www.mol.biol.ethz.ch/wuthrich/software/molmol VMD LINUX,SGI,SUN,HP,IBM,DEC www.ks.uiuc.edu/Research/vmd/ RASTER3D DEC,SGI,ESV,SUN,IBM,LINUX www.bmsc.washington.edu/raster3d/raster3d.html MAGE MAC,UNIX,LINUX,WINDOWS www.faseb.org/protein/ProSciDocs/ MageInstall.html MOLSCRIPT SGI,DEC,LINUX www.avatar.se/molscript/molscript.html CN3D Windows,MAC,UNIX www.ncbi.nlm.nih.gov/Structure/cn3d.html MIDAS I simply could not find this one! INTERCHEM SGI interchem.chem.strath.ac.uk/inter/interchem.html MOLNEMA Windows95 and higher/NT www.nrcgeb.ac.ir/armin WEB-LAB VIEWER Windows95/WindowsNT www.msi.com/viewer MOLEKEL SGI www.cscs.ch/Official/VisMolekel.html MOE SGI,SUN,WindowsNT, www.chemcomp.com Windows95,MAC,DEC ** MMTK as of yet has no visualization routines as of yet, but was placed in the above list for completeness. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx III) 1. MOLVIEW MolView can display two MolView files at a time. There can be multiple structures in the MolView or PDB files. MolView Lite can open several windows at a time. Yea, Rasmol might open more, but I have a lot more drawing options and parameters that I need to keep track of and to maintain memory blocks for. For example, you can do 3D alignments and such... Hope this helps... Tom Department of Biological Sciences Purdue University Lilly Hall B135 West Lafayette, IN 47907 Tel (765)494-8038 Fax (765)496-1189 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 2. GOPENMOL Hi Iraj, Sure, gopenmol can display multiple structures at the same time. You can even rotate them separately. Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Hi Iraj, gOpenMol (http://laaksonen.csc.fi/gopenmol/) can do any number of structures. The only limit is the memory available on your machine. Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 3. SWISS-PDB You can open up to 16 proteins, each coming in a separate layer. If you regroup several proteins in the same layer, then more proteins can be displayed. Nicolas xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 4. MOLDEN No molden can not do that. It really boils down to working with fortran (The Xwindowing stuff is in C). I have along term plan to switch to C altogether, and then multiple molecules would not be so hard. Regards, Gijs -- +----------------------------+-----------------------------------+ Gijs Schaftenaar, Drs. | CAOS/CAMM Center Email: schaft@caos.kun.nl | University of Nijmegen URL : http://www.caos.kun.nl/staff/schaft.html Tel. : +31 24 3653369 | Toernooiveld 1 Fax : +31 24 3652977 | 6525 ED Nijmegen, The Netherlands +-------- CAOS/CAMM is the Dutch National Node in EMBnet --------+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 4. MMTK MMTK has no visualization routines of its own (yet). Visualization is handled via external viewers, of which the best supported is currently VMD. Unfortunately this approach does not permit feedback >from the viewer to MMTK, so interactive manipulation is not possible. That's why there will be OpenGL-based visualization code in MMTK at a later stage, but not yet! Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 5. MacMolecule2/PCMolecule2 Thank you for your inquiry. MacMolecule2 and PCMolecule2 display single PDB files per open window. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 6. MOLMOL Sure, as many as you want (until the memory runs out). I once read 2000 BPTI structures. Reto xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 8. VMD Yes. You can load multiple proteins quite easily. And you can use one of several different representations for each of them, or for parts of them if you do atom selections. John Stone vmd@ks.uiuc.edu -- Theoretical Biophysics Group Email: johns@ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!! oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo how about VMD? http://www.ks.uiuc.edu/Research/vmd/ ( a lot better than RasMol imo) -- Tim Triche v2triche@btv.ibm.com oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo VMD can do this. See http://www.ks.uiuc.edu/Research/vmd/ -Jim oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Hi, Iraj, Please check the webpage of Theoretical Biophysics group in the Beckmann Institute in UIUC, they have a package call VMD, it is free. Good luck. Dayong xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 9. RASTER3D Raster3D will display whatever you ask it to. The rendering program doesn't know anything about "proteins"; it just knows about individual spheres, cylinders, ellipsoids, surfaces, etc, that some program has grouped together to make a picture. The various pre-processing programs can convert PDB files to some combination of the above for rendering. If you want 20 proteins at once, just feed them through into the same picture. (Of course realistically if you try to put 20 side-by-side they will end up so small you can't see much.) Ethan ------------------------------------------------------------------- Ethan A Merritt K428b Health Sciences Dept of Biological Structure phone: (206)543-1421 University of Washington FAX: (206)685-7002 Seattle, WA 98195-7742 merritt@u.washington.edu ------------------------------------------------------------------- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 10. MAGE Iraj, Yes, MAGE will display multiple proteins at the same time. Perhaps of historical interest since you are at Harvard, one of the very first kinemages showed a superposition of carboxypeptidase with and without a bound inhibitor. MAGE can not only show both superimposed, but more usefully, can rapidly animate between then - giving a very clear understanding of just what moves to accommodate the substrate! Dave Richardson. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 11. MOLSCRIPT Please note that MolScript is not really an interactive display program like Rasmol. The main point with MolScript is to produce high-quality images of a protein for publication (Web or literature), not for investigating protein structures interactively. However, the direct answer to your question is yes. One can read in as many coordinate files (sets) as one likes (and fits into your computer memory). The placement of the different molecules will be a little bit tricky, since they will most likely be placed somewhere far away from the origin. So you will have to transform them closer to the center for useful results. I am not sure exactly what it is you want to do, but my advise is to just get the software and try it. -- Per Kraulis mailto:pjk@avatar.se Avatar Software AB http://www.avatar.se/ address: c/o Kraulis, Heleneborgsgatan 21C, SE-117 31 Stockholm, SWEDEN. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 12. CN3D Dear Colleague: Cn3D can multiply align sequences which are similar according to the VAST similarity algorithm. For instance if you run a search with the Structures query (http://www.ncbi.nlm.nih.gov/Structure/) and view the Structure Summary for a record you will notice links at the bottom under "Structure Neighbors". When you click this you will get similar structures as calculated by VAST, and they will be arranged in a table. You can click up to f of these and have them aligned with each other. There is more information about this under the topic Neighbors int he Cn3D documentation located at: http://www.ncbi.nlm.nih.gov/Structure/cn3dhelp.html Hope this helps. Sincerely, Scott McGinnis GenBank User Services. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 13. MIDAS Try midas. I believe the company is midassoft. YOu can do at least 10 structures. Deepak. Deepak Singh Email: desingh@syr.edu Graduate Fellow URL: http://web.syr.edu/~desingh Department of Chemistry and Biochemistry, Tel: (315) 443 1739 -- work Syracuse University (315) 472 9659 -- home 1-014 Scitech Syracuse NY 13244 Fax: (315) 443 4070 "Violence is the last resort of the incompetent". -- Salvor Hardin xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 14. INTERCHEM Dear Iraj Daizadeh, The INTERCHEM program, which is available form QCPE for $500 will allow the display and independent manipulation of 1, 2, or 4 structures. These can be small molecules or large biomolecules. Various overlaying tools are also provided. The display programs works on SGI machines only. See the website: http://interchem.chem.strath.ac.uk/inter/interchem.html Yours sincerely Peter Bladon xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 15. MOLNEMA Dear Iraj, As a part of my Pharm.D thesis about 4 years ago, I have written a program by Borland C++ 3.1 and Object Windows class library, which runs under MS Windows 3.1 and higher (95, 98 and NT) and called MOLNEMA. In this program, you can load any number of molecules (in PDB and DTMM .mol format) and easily rotate and transfer them in the space independently or together (but no bond rotation). Selection is done easily via a selection window which lists all the loaded molecules, you can also see list of residues or atoms by simply double-clicking on a molecule (like directory structure). One of the unique features of the program is that you can see molecules from top, front, left and any number of perspective views (traditional four-view presentation used in 3D modeling programs like 3D Studio), simultaneously. Molecular representation is limited to wireframe and dot-surface (the later is not implemented efficiently). At that time there was no program (at least to my knowledge) to do such things under Windows, but now I think you can find many of them (like WebLabView). We used it for manual docking of ligands into the active site of receptors. Please note that MOLNEMA is not a mature program and hence not bug free and many features not implemented. Anyway if you think MOLNEMA is appropriate for your propose, just let me know. I must state that also, currently I am working on a brand new program with many enhanced features, including: - Written completely in C++ by MS Visual Studio 97 and MFC. - Rewritten from the scratch by DA and OO design in mind. - Same four view but this time implemented in OpenGL. - Fully multi-threaded (each OpenGL view has separate thread). - Utilizes MS OLE 2.0 technology for clipboard operations. - A proprietary binary file format for loading and saving molecules. - Plug-in and file filters capability (not in the first release). - It's based on a FMC (Microsoft Foundation Class) extension dynamic link library (DL) called Molecular Graphics & Modeling Application Framework or MGMAF (also written by me) which upon release greatly simplifies developing molecular graphics and modeling applications under Windows NT and 98. At the current state, we used it successfully to put 5 subunits of 5-HT3 receptor (transmembrane ionic channel) together to form a channel (unpublished work by M. Mahmoudian, S. Dabbagh and me). Unfortunately, for the time being, I am really busy with my Ph.D. thesis and don't have enough time to complete and release it, but I will do ASA I have enough free time. Regards, Armin M. Sobhani p-------------------------------------------------------------------q | __ _________ ____ Armin M. Sobhani, Pharm.D | | / \ / _ _ \ / ____\ Ph.D Student of Pharmacology | | / \\ \\ \\ \/\ \___/_ mailto:armin@nrcgeb.ac.ir | | / /\ \\ \\ \\ \ \_____ \ URL: http://www.nrcgeb.ac.ir/armin | | ( ___ \\ \\ \\ \/____/\ \Tel: +98 21 6418310 | |( \__\_/\__\\__\\__\\__\/\_____/Fax: +98 21 6419834 | | \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6343, Tehran, IRAN | !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~! | Once you understand the universe at the atomic level everything | | else is easy. -Richard P. Feynman | b-------------------------------------------------------------------d xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 16. WEBLAB VIEWER Dear Dr. Daizadeh, Please consider using the WebLab Viewer, Molecular Simulations' 3D chemical visualization and communications software package. It is well suited for protein visualization with a host of protein specific display styles. With the WebLab Viewer you can open and see multiple windows at the same time, or load several structures into the same document, and then manipulate (rotate, translate, zoom, ...) structures independently by holding down the control key. The are two versions of the WebLab Viewer currently available for download >from MSI's web site: the ViewerLite 3.1 , and the ViewerPro 3.1. The ViewerLite is free, and the ViewerPro sells for $249 to academic customers (a free 30-Day trial version of the ViewerPro 3.1 is also available). Additionally, we are currently beta testing a new version, the ViewerPro3.2. New in the WebLab ViewerPro 3.2: - Data Table Viewer (spreadsheet-like listing of model data) - COM automation support - New usability tools (fuse, text, enhanced stereochemistry, ...) - Customizable tool bars - Much more If you would like to download the beta version of the ViewerPro 3.2, or any of the other versions of the WebLab Viewer, you can do so from the ViewerPro home page at: http://www.msi.com/viewer/ I hope you enjoy using the new version. If you have any questions or comments, please fell free to contact me directly. Sincerely, John Wintersteen Product Manager, WebLab Viewer Products Molecular Simulations Inc. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 17. MOLEKEL hello Iraj, You could try to use Molekel. This is a software developped at Geneva. It is now maintained by the federal centre of scientific calculations of Switzerland. Molekel is a freeware but it is only running on silicon graphics station, as it is using GL library. enjoy, Pascal ****************************************************************** Pascal BOULET Pascal.Boulet@chiphy.unige.ch Department of Physical Chemistry University of Geneva 30, Quai e-Ansermet 1211 Geneva 4 Switzerland tel: (00 41) (22) 702 65 77 or (00 41) (22) 702 65 32 fax: (00 41) (22) 702 65 18 and Institut de Recherche sur la Catalyse, UPR 5401 CNRS Groupe de Chimie Theorique 43, Bd du 11 Novembre 1918 69622 Villeurbanne Cedex France **************************************************************** ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Dear Iraj, yes, Molekel can do that, you can have as many molecules as you wish on the screen, and manipulate them one by one or simultaneously; you can also do orintation matching. But I no longer take care of that program, so for further information, please contact Dr. Portmann: stefan.portmann@cscs.ch. thanx for your interest peter xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 18. MOE The Chemical Computing Group software MOE can display any number of individual protein structures simultaneously. The rendering of each protein chain can be altered independantly of the others, allowing for interesting mixed-renedring displays. The structures can also be manipulated individually or in groups. If you would like to see how it looks, go to the Chemical Computing Group webpage http:\\www.chemcomp.com Chris -- Chris Williams, Ph.D. Customer Support/Applications Scientist, Chemical Computing Group, Inc. 1255 University St., Suite 1600 Montreal, Quebec CANADA H3B 3X3 Tel: (514) 393-1055 Fax: (514) 874-9538 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx From chemistry-request@www.ccl.net Tue Oct 20 12:38:16 1998 Received: from asterix.mit.edu (ASTERIX.MIT.EDU [18.63.0.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA23143 Tue, 20 Oct 1998 12:38:16 -0400 (EDT) Received: from mit.edu (localhost) by asterix.mit.edu with ESMTP (1.39.111.2/16.2) id AA161222012; Tue, 20 Oct 1998 12:46:52 -0400 Sender: conny@mit.edu Message-Id: <362CBE7B.BB613E8E@mit.edu> Date: Tue, 20 Oct 1998 12:46:51 -0400 From: Cornelia Sieber X-Mailer: Mozilla 4.06 [en] (X11; I; HP-UX B.10.10 9000/777) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: G94 problem: unconnected unit Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, Trying to do a CAS(6,6)/p-ccVTZ calculation on a rather large molecule (bigger than benzene, 352 basis fcts), G94 dies shortly after going into the MCSCF program. The error message I get is: >> *** FORTRAN I/O ERROR 914: ACCESS OF UNCONNECTED UNIT >> ATTEMPTED >> FILE: , UNIT: 6 >> ( 0) 0xc1a0068c io_ded + 0x37c [/usr/lib/pa1.1/libcl.sl] >> ( 1) 0xc1a19550 FTN_S_WSFE + 0x208 [/usr/lib/pa1.1/libcl.sl] >> ( 2) 0x0006b598 fileio_ + 0x1a98 [/machine/appl/HP/g94/l510.exe] >> ( 3) 0x0004b720 mrdpot_ + 0x50 [/machine/appl/HP/g94/l510.exe] >> ( 4) 0x0003a848 srparm_ + 0x1848 [/machine/appl/HP/g94/l510.exe] >> ( 5) 0x000107c4 rparm_ + 0xf4 [/machine/appl/HP/g94/l510.exe] >> ( 6) 0x0000abc0 mcscf_ + 0x368 [/machine/appl/HP/g94/l510.exe] >> ( 7) 0x0000a748 ml510_ + 0x70 [/machine/appl/HP/g94/l510.exe] The point where it dies and the message is the same on all machines I tried (HP, IBM), regardless whether scratch-directory and working directory was on the same physical disk or not. The machines have 256 MB memory and I have about 3 GB of scratch space available. vmstat says, there is enough memory left and there is still enough scratch space available after the run died. Does anybody have an idea, what happens here and how to get over it? Thanks, Cornelia ps. Parts of the input file as well as the last lines of the output file are appended. *************************** Dr. Cornelia Sieber Dept. Chem. Eng. MIT, Cambridge, USA email: cbauer@mit.edu *************************** --- end of the output file ---------------------------------------- NO OF BASIS FUNCTIONS = 175 NO TO BE DELETED = 0 CI Matrix Elements calculated here NO. OF CONFIGURATIONS IN REFERENCE SPACE = 1 SECONDARY SPACE = 175 TERTIARY SPACE = 175 NO. OF ORBITALS = 6 NO. OF ELECTRONS = 6 NO. OF WEIGHTS = 19 REFERENCE STATE CONFIGURATIONS ARE: 0 NO. OF CORE ORBITALS = 0 OPTION: NON-DIAGONAL HOLE LINE INTERACTIONS INCLUDED Len28= 73805 LenMCI= 39229. ENTER MCSCF PROGRAM NO. OF ORBITALS =352 NO. OF CORE-ORBITALS = 25 NO. OF VALENCE-ORBITALS = 6 NO. OF VIRTUAL-ORBITALS =321 USED ACCURACY IN CHECKING CONVEGERGENCE = .00001000 ----------------------------------------------------------- ------ input file ----------------------------------------- %mem=18000000 %chk=/tmp4/conny/cas_qp.chk #n rhf/cc-pVTZ Ground state optimization 0 1 c1 c2 c1 r3 c3 c2 r1 c1 ac1 c4 c2 r1 c1 ac1 c3 180. .... --link1-- %mem=20000000 %chk=./cas_qp.chk #n cas(6,6)/cc-pVTZ geom=allcheckpoint guess=read ----------------------------------------------------------- From chemistry-request@www.ccl.net Tue Oct 20 13:59:12 1998 Received: from leona.harvard.edu (daizadeh@leona.harvard.edu [128.103.96.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA08099; Tue, 20 Oct 1998 13:59:11 -0400 (EDT) Received: from localhost (daizadeh@localhost) by leona.harvard.edu (8.8.7/8.8.7) with SMTP id NAA21496; Tue, 20 Oct 1998 13:59:53 -0400 Date: Tue, 20 Oct 1998 13:59:53 -0400 (EDT) From: Iraj Daizadeh To: Joe Golab cc: chemistry@www.ccl.net, chemistry-request@www.ccl.net Subject: More on Mass Spectrum Software In-Reply-To: <199810201353.IAA05213@interlock.amoco.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. Please check out: Curry and Rumelhart ``MSnet: A neural network that classifies mass spectra'' {\it Tetrahedron Comput. Methodol.} {\bf 3} (1990): 213-237. Lohninger ``Classification of mass spectral data using neural networks'' {\it Software Development in Chemistry} {\bf 5} Ed: J. Gmehling. Springer-Verlag (1991). Gasteiger, X et al. ``Neural nets for mass and vibrational spectra'' {\it J. Mol.Struct} {\bf 292} (1993): 141-160. See Chapter 16 of ``Computer Software Application in Chemistry: 2nd edition'' by Peter Jurs: John Wiley and Sons (1996). Iraj Iraj Daizadeh, Ph. D. Harvard University Department of Chemistry and Chemical Biology 12 Oxford Street, Box #35 Cambridge, MA 02138-2902 Phone: 617-495-2654 Fax: 617-495-1823 email: daizadeh@lhasa.harvard.edu