From raman@bioc01.uthscsa.edu Thu Jun 10 18:21:45 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306110421.AA09845@bioc01.uthscsa.edu> Subject: MOLECULAR VISUALIZATION - Proteins To: chemistry@ccl.net Date: Thu, 10 Jun 1993 23:21:45 -0500 (CDT) Dear Netters Here are some more programs that can be added to the list I posted some time ago, under the same subject heading! 1. TOM (discussed in Cindy Fisher's posting) is available via FTP from Chemi2.ucsd.edu in the directory /pub/tom/ This works quite well on SGI platforms and is used frequently in most crystallography labs. 2. MMS This program is also available from the site mentioned above in the directory /pub/mms/. In my opinion, this is an excellent program for viewing and modelling proteins. The interface is quite good (I run it on a SGI Indigo XS/24) and produces excellent output, including balck and white postscript suitable for publication. You might remember my discussion regarding MOLSCRIPT being used extensively for the latter. Steve Dempsey wrote and maintained this program, but Mark Israel at UA, Edmonton has recently made some modifications and is distributing the same. 3. RASTER 3D: As the name implies this program produces good quality raster (space filling) strucuture of proteins. The input being a PDB file. There are different versions of this software as the README file would tell you from the following site: by anon. FTP stanzi.bchem.washington.edu the programs are in /pub. These programs are highly recommended to those interested in modelling protein structures. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From EWING@JCVAXA.JCU.EDU Fri Jun 11 04:18:00 1993 Date: Fri, 11 Jun 1993 09:18 EST From: "DAVID W. EWING (216) 397-4742" Subject: Restricted vs. Unrestricted semi-empirical methods To: chemistry@ccl.net Message-Id: <01GZ8WG6D9G08Y5678@jcvaxa> Dear Computational Colleagues: We're looking at some systems with doublet spin states using MOPAC5. Our previous work on some of these systems using ab initio methods told us that some of the wavefunctions are significantly spin contaminated ( about 1.0). Question: should we stick to restricted MNDO, MINDO/3, etc. or is it "safe" to use the unrestricted methods? The question arises because we are seeing significantly different results restricted vs. unrestricted. Thank you in advance for any insight you can give into this question! Dave Ewing John Carroll University ewing@jcvaxa.jcu.edu From DSMITH@uoft02.utoledo.edu Fri Jun 11 04:01:07 1993 Date: Fri, 11 Jun 1993 09:01:07 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: MD mailing lists To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu Message-Id: <01GZ8VN0FM1E0009N4@UOFT02.UTOLEDO.EDU> There has recently been a lot of talk about yet another mail exploder, this one specific to molecular dynamics (MD). WHY????? The Chemistry mail exploder from OSC is _NOT_ limited to quantum mechanics. It has no real mandate or specifications as to allowable topics (with the fuzzy exception of commercials and sales pitches sans science). Why don't we just use the existing list, which has something over 2000 subscribers worldwide (Jan - please correct me if I am way off). In addition, I run a MacroModel mail exploder, much smaller and less active than Jan's, but specific to Still's MacroModel program. Occassionally MD questions and discussions appear there, since MacroModel is a force field based MM/MD program. I am sure that similar discussions appear on the Biosym mail exploder and others with which I may not be familiar. I have nothing against another exploder, but cross-posting becomes a problem and it is too easy to miss important discussions due to a fear of over- subscribing to these things. Let's use what we have to capacity first, IMHO. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From V098Q3NV@ubvms.cc.buffalo.edu Tue Jun 11 06:01:31 1993 Date: 11 Jun 1993 10:01:31 -0400 (EDT) From: V098Q3NV@ubvmsb.cc.buffalo.edu Subject: IBM color plotter driver for MS Win3.1 To: chemistry@ccl.net Message-Id: <01GZ8XNOLR9E8WVZOK@ubvms.cc.buffalo.edu> Organization: University at Buffalo Excuse the bandwidth... Anybody have any experience using an IBM 6180 color plotter with MS Windows 3.1? The Windows supplied drivers are only for HP's, and none of these are working for me. Any info regarding settings or where additional drivers may be obtained is greatly appreciated. John Manchester Dept of Biophysics Roswell Park Cancer Institute Buffalo Ny 14263 716/845-4424 ph 716/845-8906 fx v098q3nv@ubvms.cc.buffalo.edu From raman@bioc01.uthscsa.edu Fri Jun 11 11:29:32 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306112129.AA10302@bioc01.uthscsa.edu> Subject: Re: MD mailing lists To: DSMITH@uoft02.utoledo.edu (DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO) Date: Fri, 11 Jun 1993 16:29:32 -0500 (CDT) The idea behind the PMD mailing list is not to create a separate MD oriented mail exploder, but to bring together users of md and pmd programs to exchange ideas and improvements. I already stated this in my previous posting. There are quite a few who don't subscribe to this mailing list, but are interested in discussing MD! So, the pmd list will not only discuss issues pertaining to the program, but also, other molecular dynamics related items. For the sake of brevity, let me conclude by saying that this new mail exploder is not going to take away anything from the discussion we have here! -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************