From raman@bioc01.uthscsa.edu Sun Apr 11 06:26:08 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9304111626.AA17557@bioc01.uthscsa.edu> Subject: Molecular Visualization Packages To: chemistry@ccl.net Date: Sun, 11 Apr 1993 11:26:08 -0500 (CDT) I found that some of the MOST IMPORTANT packages available for visualization of MOLECULES were not mentioned in an earlier posting. Here I include a small description and my thoughts on the same: 1. For PROTEIN, DNA and SMALL MOLECULE visualization THE best package I have seen so far is called RIBBONS and it is OUTSTANDING. The graphics are fantastic and pictures captured from the screen can be used for producing slides or plates for publication. PLATFORMS: currently SGI and ESV workstations. Other ports may be in the works. AVAILABILITY: Academic institutions can license it for a small fee from Dr. Mike Carson, Centre for Macromolecular Crystallography, UAB; his email: carson@gtx.cmc.uab.edu HIGHLY RECOMMENDED! 2. For those interested in submitting BLACK & WHITE protein strucutures for publication, with 100's of grey level shades, THE best available software is MOLSCRIPT. OUTPUT: most beautiful POST-SCRIPT (black and white!) figures. PLATFORMS: I know of the SGI version that we run, but other ports may be available. AVAILABILITY: This significant contribution to the field of visualization software was written by Dr. Per Kraulis at the Department of Biochemistry, University of Cambridge, UK. His email isn't available for distribution but anyone interested in this can contact me for more information! HIGHLY RECOMMENDED! 3. MIDAS PLUS - not only has visualization capabilities, but also manipulation, comparison, surface areas and many other capabilities of interest to scientists in PROTEIN SCIENCE. The graphics quality is excellent and so are its other features. PLATFORMS: SGI with hardware Z buffer option. AVAILABILITY: via The University of California , San Francisco; Computer Graphics Laboratory; a small licensing fee for Academics. HIGHLY RECOMMENDED! 4. AMBER - exclusively for molecular dynamics and energy minimization calculations of biomolecules. The latest version is quite good in its capabilities. PLATFORMS: SGI ; but others may be available AVAILABILITY: via UCSF; from Dr. Peter Kollman. 5. PCMAGE & MACMAGE : For those of you who are not workstation oriented but would like a package that is freely available in the public domain for both PC's and Mac's. This software was developed for distribution with the journal Protein Science (Editor: Hans Neurath; former Chief editor of BIOCHEMISTRY) has now been made available through anon FTP sites. Use archie to find them. One of the sites that I remember where these packages can be found is *.uci.edu 6. XTALVIEW - This package was briefly mentioned in an earlier posting to this newsgroup. It has undergone some major revision since December 1992 and is a must if you are interested in crystallography. With respect to visualization capabilities, it can handle PEPTIDE PLANES, Ramachandran Plots, Hydrogen Bonds, C-alpha backbone, representation and mapping of side chains, atom-atom distances, measurement of torsion angles etc and is PROTEIN STRUCTURE ORIENTED. The interface is by means of the standard Xlib (Xview), thus making it easily portable to other architechtures. PLATFORMS: SUN, SGI AVAILABILITY: from the author of the program Dr. Duncan Mcree, a cyrstallographer himself, at the Scripps Research Institute, La Jolla. email: dem@scripps.edu It can be licensed for a small fee from the author. I believe that the pre 12/92 version for SUN and SGI platforms (binaries) are available for downloading via FTP: perutz.scripp.edu ; make sure that you also obtain the documentation in post-script format: xvguide.ps. HIGHLY RECOMMENDED! I have personally tested and run all the above mentioned software with wonderful results. All of them came with excellent instructions on handling data and a little time spent on them can produce marvelous results! I would be happy to answer any specific questions, should they arise! -- 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 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 ******************************************************************************