From chemistry-request@server.ccl.net Wed Jun 16 14:37:51 1999 Received: from unet.univie.ac.at (unet.univie.ac.at [131.130.230.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA14585 for ; Wed, 16 Jun 1999 14:37:49 -0400 Received: from brain (uvo1-80.univie.ac.at [131.130.231.80]) by unet.univie.ac.at (8.8.8/8.8.7) with ESMTP id UAA84770 for ; Wed, 16 Jun 1999 20:29:42 +0200 Received: from 192.168.0.1 by brain ([192.168.0.1] running VPOP3) with SMTP for ; Wed, 16 Jun 1999 20:25:47 +0200 Message-ID: <002501beb825$a74acaf0$0100a8c0@brain> Reply-To: "Alexander Klinsky" From: "Alexander Klinsky" To: Subject: SOMFA Download location Date: Wed, 16 Jun 1999 20:25:47 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 X-Server: VPOP3 V1.3.1 - Registered to: Lukundoo [HPA] Dear All ! For all of you trying to download SOMFA 2.0 from the web try this instead: ftp://fangio.pcl.ox.ac.uk/ftproot/somfa2.zip Cheers, Alexander Klinsky Institute of Theoretical Chemistry University of Vienna Austria From chemistry-request@server.ccl.net Thu Jun 17 05:13:24 1999 Received: from www0r.netaddress.usa.net (www0r.netaddress.usa.net [204.68.24.47]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA21515 for ; Thu, 17 Jun 1999 05:13:23 -0400 Received: (qmail 2662 invoked by uid 60001); 17 Jun 1999 09:05:17 -0000 Message-ID: <19990617090517.2661.qmail@www0r.netaddress.usa.net> Received: from 204.68.24.47 by www0r via web-mailer(M3.2.0.17) on Thu Jun 17 09:05:17 GMT 1999 Date: 17 Jun 99 10:05:17 BST From: Kevin Kincaid To: chemistry@ccl.net Subject: Summary : Orbital Viewer for Jaguar. X-Mailer: USANET web-mailer (M3.2.0.17) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA21516 Hi All! Below is a summary of the replies to my query re. Orbital Viewers for Jaguar. Thanks very much to every one who replied. Kevin. -------Summary Starts------------ Kevin, As long as you're not using any ECP basis sets then I'm pretty sure that Spartan from Wavefunction can visualize the orbitals from jaguar. My problem is that I use ECP basis sets, so I'm interested in any responses others might provide. thanks, Davis Reichert ---------------------- Hi: I know a good one for view result from jaguar. The address is the following: http://zarbi.chem.yale.edu/~lim/xchemedit/brochure/overview.html Hope it will help you. Mao Xiang --------------------- I tried to get more information on this, but so-far no reply. --------------------- Dear Kevin Serenasoft - the maker of PCMODEL have such a program it' called orbdraw and runs under WINNT - it's not free though ($200) Check out: http://www.serenasoft.com/orbdraw.html Best wishes Peter --------------------- I know Richard P. Muller from schrodinger has experimented with the molden_format in order to interface Jaguar with molden, but i dont know wether it got to the stage of a working program/script. (e-mail: rpm@wag.caltech.edu) Best Regards, Gijs Schaftenaar -------------------- And in reply to this …. --------------------- Kevin, I wrote a Perl file that converts the Jaguar restart file to the .molf format. You can find that at http://www.wag.caltech.edu/home/rpm/molden I'm also working on a solution that doesn't use Molden, which I've found to be a bit slow. Right now it's still in development, but I've been using Python, in conjunction with the VTK graphics toolkit. If you go to the web page http://www.wag.caltech.edu/home/rpm/python you can see some of the things I've been working on. The orbital stuff is in http://www.wag.caltech.edu/home/rpm/orbitals.html. I believe that all of the scripts are online. If you have trouble with any of this let me know, and I'll be glad to help. Rick --------------------- molden can be found at : http://www.caos.kun.nl/~schaft/molden/molden.html --------------------- Two things of interest... Spartan can display Jaguar orbitals (but not available on Linux). Titan, a new program to be released later this summer, will combine Spartan and Jaguar. So you will have Spartan's graphical interface (building, set up, display) + Jaguar's computational engine in a single package. The folks at Schrodinger and Wavefunction can tell you more. -Alan --------------------- A reply from the folks at Schrodinger ….. -------------------- We are indeed working with Wavefunction, Inc. to co-create the Titan product. The product is in testing right now and will make its debut at WATOC in London in about 1.5 months (Aug 2). Would you be attending the WATOC by chance? If so, do come by the exhibit for a demo. Titan is a Windows product, running on PC's running Windows 95/98/NT. Best regards, Shi-Yi -----Summary ends------ ____________ Kevin Kincaid chemistry.forums@usa.net Dublin City University, Ireland ____________________________________________________________________ Get free e-mail and a permanent address at http://www.netaddress.com/?N=1 From chemistry-request@server.ccl.net Thu Jun 17 12:56:49 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27419 for ; Thu, 17 Jun 1999 12:56:44 -0400 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id NAA39107; Thu, 17 Jun 1999 13:47:31 -0300 Date: Thu, 17 Jun 1999 13:47:31 -0300 (BSC) From: andre mauricio de oliveira To: Alexander Klinsky cc: CHEMISTRY@server.ccl.net Subject: Re: CCL:SOMFA2 TF2 Files Problems In-Reply-To: <001901beb812$21a29da0$0100a8c0@brain> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr Klinsky, If you have program Tsar(TM) installed in any workstation, you can use it to export structures as .css, which samfa2 will easily read. I have notice the same problems you reported, and this was the only solution I have found. On Wed, 16 Jun 1999, Alexander Klinsky wrote: > Dear Colleagues ! > > > We have just begun using SOMFA2 and were unfortunately not able to generate > the required tf2 files from our structures which are available as pdb files > after superpositioning. > > We did the following without success: > > 1. Convert the PDB file to CSSR Format using Babel 1.6 then convert it with > the included conversion utility -> Error message: Fractional coordinates not > supported > 2. Generate a CSSR file using molden 3.5 -> The same error message > > > Does anybody know the detailed structure of the tf2 files or how to generate > such files form PDB or anything else. > > Kind regards, Alexander Klinsky > Institute of theoretical chemistry > University of Vienna > Austria > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Best wishes, Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Thu Jun 17 13:49:00 1999 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA28338 for ; Thu, 17 Jun 1999 13:49:00 -0400 Received: from paris.ks.uiuc.edu (paris.ks.uiuc.edu [130.126.120.10]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with SMTP id MAA10530 for ; Thu, 17 Jun 1999 12:41:04 -0500 (CDT) Message-Id: <199906171741.MAA10530@havana.ks.uiuc.edu> Received: by paris.ks.uiuc.edu (NX5.67e/NX3.0X) id AA06007; Thu, 17 Jun 99 12:40:50 -0500 Content-Type: text/plain Mime-Version: 1.0 (NeXT Mail 3.3risc v118.3) X-Nextstep-Mailer: Mail 3.3 (Enhance 1.2) Received: by NeXT.Mailer (1.118.3) From: Dorina Kosztin Date: Thu, 17 Jun 99 12:40:49 -0500 To: chemistry@ccl.net Subject: density maps Reply-To: Dorina Kosztin Dear All, I would greatly appreciate if somebody will point out for me a program that takes a DCD (trajectory file obtained from a molecular dynamics simulation using XPLOR or CHARMM) or multiple pdb files and builds a density map for the solvent surrounding the protein. The program can run on SGI, HP, Sun or PC, it doesn't realy matter. Thank you, Dorina Kosztin --------------------------------------------------------- Theoretical Biophysics Group Email: dorina@ks.uiuc.edu Beckman Institute, UIUC Phone: (217) 244-8946 405 North Mathews Ave. Fax: (217) 244-6078 Urbana, IL 61801, USA http://www.ks.uiuc.edu/ ---------------------------------------------------------