From parthi@aero.iisc.ernet.in Wed May 14 01:43:00 1997 Received: from milan.doe.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id BAA08436; Wed, 14 May 1997 01:19:29 -0400 (EDT) Received: from iisc.ernet.in by milan.doe.ernet.in (4.1/SMI-4.1) id AA28701; Wed, 14 May 97 10:47:48+050 Received: from aero.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id KAA14101; Wed, 14 May 1997 10:42:47 +0530 Received: by aero.iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA04264; Wed, 14 May 1997 10:40:58 -0500 Date: Wed, 14 May 1997 10:40:58 -0500 (GMT) From: S Parthiban To: Iraj Daizadeh Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:3-D Imaging In-Reply-To: <9705130948.ZM20103@indigo.ucdavis.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Hello. > > Would anyone know an easy-to-learn program that allows for visualizing data > from a file in 3-dimension Euclidean space something that looks like a fluid > dynamics simulation? I started to write such a piece of code using Tcl/Tk but > speed is of the essence (as always). > Thanks in advance. > Iraj Daizadeh IBM visualization data explorer/IRIS explorer will do. A while ago, i downloaded the comparison of these visualization softwares. Now I dont remember the URL. But u can find them in my homepage. http://144.16.73.100/~parthi/home.html and CLICK "visualization". u can see the comparison of four visualization softwares. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= S. PARTHIBAN =-= =-= Supercomputer Education and Research Center =-= =-= Indian Institute of Science, Bangalore-560012, INDIA =-= =-= =-= =-= E-Mail: parthi@aero.iisc.ernet.in =-= =-= http://144.16.73.100/~parthi/home.html =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From ccchuang@gate.sinica.edu.tw Wed May 14 03:43:02 1997 Received: from gate.sinica.edu.tw for ccchuang@gate.sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id DAA08958; Wed, 14 May 1997 03:05:19 -0400 (EDT) Received: by gate.sinica.edu.tw (SMI-8.6/SMI-SVR4) id PAA07440; Wed, 14 May 1997 15:04:28 +0800 Date: Wed, 14 May 1997 15:04:27 +0800 (CST) From: Chyh-chong Chuang To: CHEMISTRY@www.ccl.net Subject: Pratical question about Tripos's Composer In-Reply-To: <199705140700.PAA07103@gate.sinica.edu.tw> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netter: I am using tripos's Composer for homology modeling work. In my case, I have 2 templates. Base on these two template, I assigned several SCRs. And among them, there is a pair of alpha helix which should be SCR having slightly different orientation. And it is the longer loop which cause the helix move out. In Composer, the frame was built base on all the templates. But In my case, in this SCR helix, I prefer to use one of the helix but not the averaged frame. How to do this in Composer? Any suggestion/help will be greatly appreciated. Thank you very much. ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From ccchuang@gate.sinica.edu.tw Wed May 14 03:51:59 1997 Received: from gate.sinica.edu.tw for ccchuang@gate.sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id DAA08965; Wed, 14 May 1997 03:05:56 -0400 (EDT) Received: by gate.sinica.edu.tw (SMI-8.6/SMI-SVR4) id PAA07548; Wed, 14 May 1997 15:06:07 +0800 Date: Wed, 14 May 1997 15:06:06 +0800 (CST) From: Chyh-chong Chuang To: CHEMISTRY@www.ccl.net Subject: Tripos's Composer! How to seperately model 2 lobes in a protein? In-Reply-To: <199705140700.PAA06854@gate.sinica.edu.tw> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I have a protein homology modeling work at hand. This protein can be divided into 2 lobes, N terminal lobe and C terminal lobe, and the 2 lobes are connected by a short loop sequence. Comparing the structures of the templates, I found that the overall superimposion of the whole proteins is not good. But if I seperately superimposed the N lobe or C lobe, the superimposion is good. So I plan to do a model by seperately modeling the N lobe and C lobe and then connecting the 2 lobes by loop. I used different run to separately model the N and C lobe. My question is that how to combine the two run in a single running so that I can do the loop modeling? Any comment/suggestion/help will be great appreciated. Thank you very much. Sincerely your ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From parthi@aero.iisc.ernet.in Wed May 14 03:58:18 1997 Received: from milan.doe.ernet.in for parthi@aero.iisc.ernet.in by www.ccl.net (8.8.3/950822.1) id DAA08974; Wed, 14 May 1997 03:07:33 -0400 (EDT) Received: from iisc.ernet.in by milan.doe.ernet.in (4.1/SMI-4.1) id AA02392; Wed, 14 May 97 12:41:47+050 Received: from aero.iisc.ernet.in by iisc.ernet.in (ERNET-IISc/SMI-4.1) id KAA14101; Wed, 14 May 1997 10:42:47 +0530 Received: by aero.iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA04264; Wed, 14 May 1997 10:40:58 -0500 Date: Wed, 14 May 1997 10:40:58 -0500 (GMT) From: S Parthiban To: Iraj Daizadeh Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:3-D Imaging In-Reply-To: <9705130948.ZM20103@indigo.ucdavis.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Hello. > > Would anyone know an easy-to-learn program that allows for visualizing data > from a file in 3-dimension Euclidean space something that looks like a fluid > dynamics simulation? I started to write such a piece of code using Tcl/Tk but > speed is of the essence (as always). > Thanks in advance. > Iraj Daizadeh IBM visualization data explorer/IRIS explorer will do. A while ago, i downloaded the comparison of these visualization softwares. Now I dont remember the URL. But u can find them in my homepage. http://144.16.73.100/~parthi/home.html and CLICK "visualization". u can see the comparison of four visualization softwares. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =-= S. PARTHIBAN =-= =-= Supercomputer Education and Research Center =-= =-= Indian Institute of Science, Bangalore-560012, INDIA =-= =-= =-= =-= E-Mail: parthi@aero.iisc.ernet.in =-= =-= http://144.16.73.100/~parthi/home.html =-= =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Gerald.Loeffler@univie.ac.at Wed May 14 09:43:04 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id JAA10838; Wed, 14 May 1997 09:16:08 -0400 (EDT) Received: from gerilap.imp.univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id PAA07868; Wed, 14 May 1997 15:15:49 +0200 Message-ID: <3379B92A.7797@univie.ac.at> Date: Wed, 14 May 1997 15:07:54 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List , Gerald Loeffler Subject: SUMMARY: Numerically Solving Partial Differential Equations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! The following books dealing with numerical solutions to partial differential equations were recommended to me. Thanks to all who responded - you know who you are! The list of books: o "Numerical Recipes in ". also online at http://cfata2.harvard.edu/numerical-recipes. o Lapidus L. & Pinder G.F., "Numerical Solution of Partial Differential Equations in Science and Engineering", Wiley, New York, 1982 o Smith G.D., "Numerical Solution of Partial Differential Equations: Finite Difference Methods" (3rd edition), Clarendon, Oxford, 1985. "Numerical Recipes" cites (among many others): o W. Hackbusch, "Multi-Grid Methods and Applications", Springer, New York, 1985 o L. Baker, "More C Tools for Scientists and Engineers", McGraw-Hill, New York, 1991 o W. L. Briggs, "A Multigrid Tutorial", S.I.A.M., Philadelphia, 1987 o W. Hackbusch and U. Trottenberg (eds.), "Multigrid Methods III", Birkhauser, Boston, 1991 Furthermore, poeple noted that: o "Finite difference" means "finite element" with box-shaped elements. o Chris Cortis (chris@boreale.bioc.columbia.edu) wrote a program called PBSOLV that does essentially what Delphi does (i.e, solve the Poisson-Boltzmann equation) but uses finite element methods instead of finite difference methods. It gives forces as well as energies. -- Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From stephen_andruski@fmc.com Wed May 14 10:43:08 1997 Received: from igw.fmc.com for stephen_andruski@fmc.com by www.ccl.net (8.8.3/950822.1) id KAA11302; Wed, 14 May 1997 10:31:05 -0400 (EDT) Received: by igw.fmc.com id AA12162 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 14 May 1997 09:31:07 -0500 Message-Id: <199705141431.AA12162@igw.fmc.com> Received: by igw.fmc.com (Internal Mail Agent-1); Wed, 14 May 1997 09:31:07 -0500 Mime-Version: 1.0 Date: Wed, 14 May 1997 08:54:43 -0500 From: stephen_andruski@fmc.com (STEPHEN ANDRUSKI) Subject: Re: Print quality images To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part ORTEP for Window 95 reads XYZ files directly and will create a ball and stick line drawing in color or black and white. It will also automatically label the atoms and you can reposition the labels interactively. The program is free off the net, unfortunately I am travelling and I don't have the URL for the site with me. Check the main ORTEP site and go from there. Steve Andruski FMC Corporation stephen_andruski@fmc.com From redime@azur.incm.u-nancy.fr Wed May 14 11:43:07 1997 Received: from brown.incm.u-nancy.fr for redime@azur.incm.u-nancy.fr by www.ccl.net (8.8.3/950822.1) id LAA11630; Wed, 14 May 1997 11:04:25 -0400 (EDT) Received: from azur.incm.u-nancy.fr by brown.incm.u-nancy.fr via ESMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA03621; Wed, 14 May 1997 17:03:51 +0100 Received: (from redime@localhost) by azur.incm.u-nancy.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) id QAA13513; Wed, 14 May 1997 16:53:50 +0100 From: "Redime HADJI" Message-Id: <9705141653.ZM13511@azur.incm.u-nancy.fr> Date: Wed, 14 May 1997 16:53:50 -0400 In-Reply-To: Bill Davis "CCL:micelles" (May 13, 11:53am) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: CCL:micelles Cc: bdavis@YorkU.CA Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On May 13, 11:53am, Bill Davis wrote: > Subject: CCL:micelles > Hi everyone! > > Does anyone know if there is any published work on the stability of > micelles or reverse micelles in liquid media. More specifically, their > stability when the liquid boils? Thanks for the help. > > Regards, Check D. Brown and J.H.R. Clarke , MOLECULAR DYNAMICS SIMULATION OF A MODEL RESERVE MICELLE, J.Phys.Chem, 1988, 92, 2881-2888. Refences to other works may be found in that paper. -- oooooooooooooooooooooooooooooooooooooooooooooooooooooo Redime HADJI-PFEFFER redime@incm.u-nancy.fr Lab. Chimie theorique Univers. NancyI, France tel:+33-(0)3.83.91.20.00 poste : 32.70 fax:+33-(0)3.83.91.25.30 La vie est belle et c'est tant mieux J.-J. Vanier oooooooooooooooooooooooooooooooooooooooooooooooooooooo From elewars@alchemy.chem.utoronto.ca Wed May 14 11:52:14 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA11766; Wed, 14 May 1997 11:35:14 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA22344 for chemistry@www.ccl.net; Wed, 14 May 1997 11:35:15 -0400 (EDT) Date: Wed, 14 May 1997 11:35:15 -0400 (EDT) From: "E. Lewars" Message-Id: <199705141535.LAA22344@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: MOLECULE DRAWING FROM XYZ--REPLY 1997 May 14 Hello, This is in response to a question about a program that will accept molecular geometry in XYZ format and give nice pictures (a drawing program). The Windows program Molwin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. MolWin will accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. E. Lewars ==== From BISETTYK@wpogate.mlsultan.ac.za Wed May 14 12:43:07 1997 Received: from Raven.und.ac.za for BISETTYK@wpogate.mlsultan.ac.za by www.ccl.net (8.8.3/950822.1) id MAA12112; Wed, 14 May 1997 12:42:47 -0400 (EDT) Received: from wpogate.mlsultan.ac.za (wpogate.mlsultan.ac.za [196.13.102.11]) by Raven.und.ac.za (8.8.3/8.7.3) with SMTP id SAA07957 for ; Wed, 14 May 1997 18:42:41 +0200 (SAT) From: "KRISHNA BISETTY" To: Chemistry@www.ccl.net Date: Wed, 14 May 1997 18:25:00 +200 Subject: Request X-Gateway: iGate, (WP Office) vers 4.04c - 1009 MIME-Version: 1.0 Message-Id: <3379E7E9.04B3.0000@wpogate.mlsultan.ac.za> Content-Type: TEXT/PLAIN; Charset=US-ASCII Content-Transfer-Encoding: 7BIT Dear computational chemists, I am presently using G92W and HyperChem for the calculations of some small peptides at the semi-empirical and ab intio levels. I would be very grateful to hear from colleagues who have made modifications of the Hamiltonian, while trying to obtain optimization of parameters for semiempirical methods. What I actually need is for someone to please show me how to make changes to the semi-empirical parameters included in HyperChem. Any suggestions/hints ets., would be greatly appreciated. Best wishes ------------------------------------------------------------------------------------- Vincent Bisetty Department of Chemistry ML Sulatn Technikon Durban South Africa Bisettyk@wpo.mlsultan.ac.za Tel +27-31-3085312 fax +27-31-3085400 ----------------------------------------------------------------------------------------- From elewars@alchemy.chem.utoronto.ca Wed May 14 14:43:07 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id OAA13306; Wed, 14 May 1997 14:26:28 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id OAA15080 for chemistry@www.ccl.net; Wed, 14 May 1997 14:26:29 -0400 (EDT) Date: Wed, 14 May 1997 14:26:29 -0400 (EDT) From: "E. Lewars" Message-Id: <199705141826.OAA15080@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: DRAWING PROGRAM--REPLY 1997 May 14 Hello, This is in response to a question about a program that will accept molecular geometry in XYZ format and give nice pictures (a drawing program). The Windows program Molwin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. MolWin will accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. E. Lewars ==== From roussea@uia.ua.ac.be Wed May 14 15:06:54 1997 Received: from inch.uia.ac.be for roussea@uia.ua.ac.be by www.ccl.net (8.8.3/950822.1) id OAA13253; Wed, 14 May 1997 14:19:01 -0400 (EDT) Received: from struct4.uia.ac.be by inch.uia.ac.be; (8.8.5/1.1.8.2/22Feb95-0943AM) id QAA07596; Wed, 14 May 1997 16:40:57 +0200 (MET DST) Sender: roussea@uia.ua.ac.be Message-ID: <3379CE2B.167E@uia.ac.be> Date: Wed, 14 May 1997 16:37:31 +0200 From: Bart Rousseau Organization: University of Antwerp X-Mailer: Mozilla 3.0Gold (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Problem with an MP2 calculation using G94 Content-Type: multipart/mixed; boundary="------------2781446B794B" This is a multi-part message in MIME format. --------------2781446B794B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, We did an MP2 calculation (see attached input file) and tried to calculate Trace(PS) where P is the MP2 density matrix and S the overlap matrix. This should of course be equal to N, the total number of electrons. For our system which has 20 electrons we get a value of 19.383 instead of 20. Does anybody know what went wrong? Or have we missed something? Thanks in advance, Bart. ps We use G94 Rev D.4 on a Digital AlphaStation running Digital UNIX 4.0B. -- ----------------------------------------------- |Bart Rousseau, Ph.D. student | |University of Antwerp - Dep. of Chemistry | |Structural Chemistry - Quantum Chemistry | |Universiteitsplein 1 - 2610 Antwerpen | |Belgium - roussea@uia.ac.be | |http://sch-www.uia.ac.be/struct/quantum/ | |kobalt@innet.be - Bart.Rousseau@kava.be| |Tel.: + 32 3 8202366 - Fax.: + 32 3 8202356 | ----------------------------------------------- --------------2781446B794B Content-Type: text/plain; charset=us-ascii; name="abcd.com" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="abcd.com" %Mem=128MB %Chk=abcd.chk #P RMP2(Full,FullDirect)/Gen Density=current Units=au Pop=Full Test Test 3-21G 0 1 H 0.0042351 -1.4679457 1.2424573 N -0.0563628 0.3422276 0.7070346 Li -1.6080807 1.2276114 1.3197142 F 1.5279278 1.2776066 1.1338566 H 0 S 2 1.00 0.5447178000D+01 0.1562850000D+00 0.8245472400D+00 0.9046910000D+00 S 1 1.00 0.1831915800D+00 0.1000000000D+01 **** N 0 S 3 1.00 0.2427660000D+03 0.5986570000D-01 0.3648510000D+02 0.3529550000D+00 0.7814490000D+01 0.7065130000D+00 S 2 1.00 0.5425220000D+01 -0.4133010000D+00 0.1149150000D+01 0.1224420000D+01 S 1 1.00 0.2832050000D+00 0.1000000000D+01 P 2 1.00 0.5425220000D+01 0.2379720000D+00 0.1149150000D+01 0.8589530000D+00 P 1 1.00 0.2832050000D+00 0.1000000000D+01 **** Li 0 S 3 1.00 0.3683820000D+02 0.6966860000D-01 0.5481720000D+01 0.3813460000D+00 0.1113270000D+01 0.6817020000D+00 S 2 1.00 0.5402050000D+00 -0.2631270000D+00 0.1022550000D+00 0.1143390000D+01 S 1 1.00 0.2856450000D-01 0.1000000000D+01 P 2 1.00 0.5402050000D+00 0.1615460000D+00 0.1022550000D+00 0.9156630000D+00 P 1 1.00 0.2856450000D-01 0.1000000000D+01 **** F 0 S 3 1.00 0.4138010000D+03 0.5854830000D-01 0.6224460000D+02 0.3493080000D+00 0.1343400000D+02 0.7096320000D+00 S 2 1.00 0.9777590000D+01 -0.4073270000D+00 0.2086170000D+01 0.1223140000D+01 S 1 1.00 0.4823830000D+00 0.1000000000D+01 P 2 1.00 0.9777590000D+01 0.2466800000D+00 0.2086170000D+01 0.8523210000D+00 P 1 1.00 0.4823830000D+00 0.1000000000D+01 **** --------------2781446B794B-- From psv8b@watt.seas.virginia.edu Wed May 14 15:43:10 1997 Received: from mail.virginia.edu for psv8b@watt.seas.virginia.edu by www.ccl.net (8.8.3/950822.1) id PAA13959; Wed, 14 May 1997 15:42:13 -0400 (EDT) Received: from watt.seas.virginia.edu by mail.virginia.edu id aa11227; 14 May 97 15:42 EDT Received: from localhost (psv8b@localhost) by watt.seas.Virginia.EDU (8.8.5/8.6.6) with SMTP id PAA440856 for ; Wed, 14 May 1997 15:42:11 -0400 Date: Wed, 14 May 1997 15:42:11 -0400 (EDT) From: "Venkataraman P.S." Reply-To: "Venkataraman P.S." To: chemistry@www.ccl.net Subject: Re; SUMMARY : Software for print quality images Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Thanks for the overwhelming response to my query. The Original query was as follows (in abridged form) : "I am looking for a "free" software that would read XYZ co-ordinates of molecules and produce print quality images in black & white. The software should preferably have the following additional features : ..." The softwares suggested for the above purpose include: MSI's WebLab Viewer http://www.msi.com/weblab/ Chem3D http://www.camsci.com XMol http://www.msc.edu/msc/docs/xmol/ moviemol http://www.kvac.uu.se/~lars/moviemol.html VMD http://www.ks.uiuc.edu/Research/vmd xbs http://www.ihp-ffo.de/~msm molden http://camms1.caos.kun.nl/~schaft/molden/molden.html MolWin oak.oakland.edu/simtel/win3/chem/molwin23.zip ORTEP for Window 95 check Web Most of the above are freeware. I tried using XMol and Moviemol and found them to be excellently suited for my purposes. VMD on the other hand , i think, is more useful to biological molecules, etc (and a pretty good one too). Chem3D is only available commercially. Their freeware is only for demo. I hope the summary is useful to those who share similar concerns. Thanks to all who responded (and apologies to those whose names got inadvertantly left out). The responses to my query are appended to this mail. Venkat ######################################################### R E S P O N S E ####################################################### ******************************************************************* I'd take a look at MSI's WebLab Viewer (http://www.msi.com/weblab/) . But I don't know how easy it is to do labels, though. And it is still not available on Silicon Graphics workstations. Leif Norskov Novo Nordisk A/S *************************************************************** I have always used Chem3D for geneating postscript files of 3D molecular structures. It is configurable to have atom labels or numbers on the atoms, exports postcript form, allows free rotation/translation of structures and fragments, and imports xyz data. There is a Macintosh freeware version of this software available from CamSci at: ____Nicholas C. DeMello, Ph.D.________________________________________ ****************************************************************** Sounds like the program you want is XMol distributed by the Minnesota Supercomputer Center. We have a version that runs on Unix based machines (SGI), but I have heard some rumors it won't run on all platforms. Check out: http://www.msc.edu/msc/docs/xmol/ Kenneth E. Lind, Graduate Student : Department of Medicinal Chemistry, University of Minnesota : ******************************************************************* in case you have a SGI or IBM/Risc workstation with GL graphics, you might want to try the "moviemol" program. See http://www.kvac.uu.se/~lars/moviemol.html for details. (or anonymous ftp from chem-ftp.mps.ohio-state.edu) Lars Ojamae and Kersti Hermansson ******************************************************************* There is a free program called VMD which runs on SGIs. It does much more than you want but I encourage you to try it, it has different rendering options and if you have a good printer, the quality of the image you get is excellent. You can take the code from an ftp site: ftp.ks.uiuc.edu and install it in about 5 min. If you want to read more about it, check the web page: http://www.ks.uiuc.edu/Research/vmd Dorina ********************************************************************* Maybe you could try 'xbs' written by Michael Methfessel. It's a Unix application, can name the atoms, and rotate/translate a structure. http://www.ihp-ffo.de/~msm/ Cheers, Mike. -- ------------------------------------------------------------------- | Mike Fearn, Tel : UK (01684) 896536 | | Room PA101, Fax : UK (01684) 896150 | | D.R.A, Malvern, | | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | ------------------------------------------------------------------- ********************************************************************** Try molden: http://camms1.caos.kun.nl/~schaft/molden/molden.html =20 Jochen ----------------------------------------------------------------------- Jochen Kuepper Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de Institut fuer Physikalische Chemie I ********************************************************************** MSI's WebLab Viewer is available free from our Web site (http://www.msi.com/weblab/). It produces colour images, but these print OK in black and white from a PC. * Andrew Tiller, PhD. * * Director, Market Development, Molecular Simulations Inc * ********************************************************************** This is in response to a question about a program that will accept molecular geometry in XYZ format and give nice pictures (a drawing program). The Windows program Molwin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. MolWin will accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. E. Lewars ************************************************************************ ORTEP for Window 95 reads XYZ files directly and will create a ball and stick line drawing in color or black and white. It will also automatically label the atoms and you can reposition the labels interactively. The program is free off the net, unfortunately I am travelling and I don't have the URL for the site with me. Check the main ORTEP site and go from there. Steve Andruski FMC Corporation stephen_andruski@fmc.com ************************************************************************ From psv8b@watt.seas.virginia.edu Wed May 14 16:03:46 1997 Received: from mail.virginia.edu for psv8b@watt.seas.virginia.edu by www.ccl.net (8.8.3/950822.1) id PAA13919; Wed, 14 May 1997 15:31:40 -0400 (EDT) Received: from watt.seas.virginia.edu by mail.virginia.edu id aa07426; 14 May 97 15:31 EDT Received: from localhost (psv8b@localhost) by watt.seas.Virginia.EDU (8.8.5/8.6.6) with SMTP id PAA339466 for ; Wed, 14 May 1997 15:31:41 -0400 Date: Wed, 14 May 1997 15:31:40 -0400 (EDT) From: "Venkataraman P.S." To: chemistry@www.ccl.net Subject: Re: SUMMARY : Software for print quality images Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Thanks for the overwhelming response to my query. The original query (abridged) was as follows : ********************************************************************** "I am looking for a "free" software that would read XYZ co-ordinates of molecules and produce print quality images in black & white. The software should preferably have the following additional features ...." ************************************************************************** This is (I think) an important concern for people in the computational chemistry area, who are looking for nice images for their publications. I hope the following summary is useful to those who share the same problem. The softwares suggested for the purpose were : WebLab Viewer http://www.msi.com/weblab Chem3D http://www.camsci.com XMol http://www.msc.edu/msc/docs/xmol moviemol http://www.kvac.uu.se/~lars/moviemol.html VMD http://www.ks.uiuc.edu/Research/vmd xbs http://www.ihp-ffo.de/~msm molden http://camms1.caos.kun.nl/~schaft/molden/molden.html MolWin oak.oakland.edu/simtel/win3/chem/molwin23.zip ORTEP Check Web Most of the above are available free of the net. I tried using XMol and moviemol for my purposes and found them to be quite useful. VMD (if i am not mistaken) is more convenient for biological structures (and a pretty good one too). Chem3D on the otherhand is a commercial software. Their freeware version is only for demo. For those of you who are interested in perusing through the responses i received, i have appended them to the end of this mail. Thanks once again for all your help (and apologies to those whose names i may have inadvertently omitted). Venkat ######################################################## R E S P O N S E S T O Q U E R Y ######################################################## ******************************************************************* I'd take a look at MSI's WebLab Viewer (http://www.msi.com/weblab/) . But I don't know how easy it is to do labels, though. And it is still not available on Silicon Graphics workstations. Leif Norskov Novo Nordisk A/S *************************************************************** I have always used Chem3D for geneating postscript files of 3D molecular structures. It is configurable to have atom labels or numbers on the atoms, exports postcript form, allows free rotation/translation of structures and fragments, and imports xyz data. There is a Macintosh freeware version of this software available from CamSci at: ____Nicholas C. DeMello, Ph.D.________________________________________ ****************************************************************** Sounds like the program you want is XMol distributed by the Minnesota Supercomputer Center. We have a version that runs on Unix based machines (SGI), but I have heard some rumors it won't run on all platforms. Check out: http://www.msc.edu/msc/docs/xmol/ Kenneth E. Lind, Graduate Student : Department of Medicinal Chemistry, University of Minnesota : ******************************************************************* in case you have a SGI or IBM/Risc workstation with GL graphics, you might want to try the "moviemol" program. See http://www.kvac.uu.se/~lars/moviemol.html for details. (or anonymous ftp from chem-ftp.mps.ohio-state.edu) Lars Ojamae and Kersti Hermansson ******************************************************************* There is a free program called VMD which runs on SGIs. It does much more than you want but I encourage you to try it, it has different rendering options and if you have a good printer, the quality of the image you get is excellent. You can take the code from an ftp site: ftp.ks.uiuc.edu and install it in about 5 min. If you want to read more about it, check the web page: http://www.ks.uiuc.edu/Research/vmd Dorina ********************************************************************* Maybe you could try 'xbs' written by Michael Methfessel. It's a Unix application, can name the atoms, and rotate/translate a structure. http://www.ihp-ffo.de/~msm/ Cheers, Mike. -- ------------------------------------------------------------------- | Mike Fearn, Tel : UK (01684) 896536 | | Room PA101, Fax : UK (01684) 896150 | | D.R.A, Malvern, | | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | ------------------------------------------------------------------- ********************************************************************** Try molden: http://camms1.caos.kun.nl/~schaft/molden/molden.html =20 Jochen ----------------------------------------------------------------------- Jochen Kuepper Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de Institut fuer Physikalische Chemie I ********************************************************************** MSI's WebLab Viewer is available free from our Web site (http://www.msi.com/weblab/). It produces colour images, but these print OK in black and white from a PC. * Andrew Tiller, PhD. * * Director, Market Development, Molecular Simulations Inc * ********************************************************************** This is in response to a question about a program that will accept molecular geometry in XYZ format and give nice pictures (a drawing program). The Windows program Molwin will accept Cartesians, Gaussian freq jobs or PDB and give attractive ball-and-stick pictures. The molecule can be rotated with a mouse and the atom and bond sizes can be adjusted. The pictures can be sent to WordPerfect and edited with bond lengths and angles, then printed for publication-quality illustrations. Unfortunately you can't _query_ Molwin for geometry. MolWin will accept Gaussian 92 freq output, show the molecule, and let you animate the vibrational frequencies. For G94, use the keyword requesting the long form of freq output. MolWin was written by Dr Pavel Ganelin of the Catholic University of America, 48ganelin@cua.edu It should be obtainable from oak.oakland.edu/simtel/win3/chem/molwin23.zip If it isn't there, look in the CCL archives or post a query to CCL. E. Lewars ************************************************************************ ORTEP for Window 95 reads XYZ files directly and will create a ball and stick line drawing in color or black and white. It will also automatically label the atoms and you can reposition the labels interactively. The program is free off the net, unfortunately I am travelling and I don't have the URL for the site with me. Check the main ORTEP site and go from there. Steve Andruski FMC Corporation stephen_andruski@fmc.com ************************************************************************