From faeder -x- at -x- jila02.Colorado.EDU Wed Feb 16 18:32:05 1994 Received: from jila02.Colorado.EDU for faeder ( ( at ) ) jila02.Colorado.EDU by www.ccl.net (8.6.4/930601.1506) id SAA07385; Wed, 16 Feb 1994 18:03:24 -0500 Received: by jila02.Colorado.EDU id AA19761 (5.65c+/IDA-1.4.4/CNS-3.2 for chemistry-0at0-ccl.net); Wed, 16 Feb 1994 16:03:23 -0700 Date: Wed, 16 Feb 1994 16:03:23 -0700 From: jim faeder Message-Id: <199402162303.AA19761' at \`jila02.Colorado.EDU> To: chemistry &$at$& ccl.net Subject: Request for Molecular Graphics Software-- Summary Here is a summary of the replies to my question about molecular graphics software for the Dec Alpha Workstation along with some comments. Thanks to everyone who replied. Some of the responses have been edited. For more information about the programs, contact the references within each entry. -jim The original query: ==> My research group has an Alpha AXP 3000 workstation and we would like ==>molecular graphics software that would allow us to visualize the results of ==>Monte Carlo and molecular dynamics simulations of small clusters (10-100 ==>atoms). We would like to have space-filling models, preferably with some ==>sort of shading, and have the capability of animating multiple frames. ==>Does anyone know of some free (or nearly free) software that might ==>accomplish these objectives? Thanks. --->1 xmol From: jesus at.at canarylab.chem.nyu.edu (Jesus M. Castagnetto Mizuaray) If you can output XYZ coordinates, maybe XMol it's for you. You can get info from xmol %! at !% msc.edu. Last time I saw it there was a working version for SGI machines, and versions for other platforms were in beta. Hope this helps. ----- Jesus M. Castagnetto Mizuaray | "Organic Chemistry: The practice Dep.of Chemistry - New York University | of transmuting vile substances 4 Washington Pl, Room 514. NY 10003 | into publications" (The Last Word- jesus %-% at %-% canarylab.chem.nyu.edu | The Ultimate Scientific Dictionary) ---> comment: Xmol is a great program. Unfortunately there is not currently a version for the Alpha. I don't know whether the authors of xmol are planning to port it to the Alpha. One other drawback is that the models are not shaded, so the pictures are not fully three-dimensional in appearance. The ability to do rotations interactively though makes it a good tool for looking at cluster structures. The xyz input format is also very easy to use. --->2 MidasPlus From: Tom Ferrin Thank you for your interest in our MidasPlus molecular modeling software. MidasPlus is a sophisticated molecular modeling system developed by the Computer Graphics Laboratory at the University of California, San Francisco. The system is used daily in a university-level research program for the display and manipulation of macromolecules such as proteins and nucleic acids. Ancillary programs allow for such features as computation of molecular surfaces and electrostatic potentials and generation of "pub- lication quality" space filling images with multiple light sources and sha- dows. Because of our own research needs, MidasPlus has been developed with an emphasis on the interactive selection, manipulation and docking of drugs and receptors. Although quite powerful in this application, the system is also somewhat specialized in this respect: it requires three dimensional atomic coordinate data for the structures being displayed and expects the primary structure to be based on linear chains of subunits such as amino acids or nucleic acids. Using MidasPlus for complex inorganic compounds or large polymers with many crosslinks is discouraged. MidasPlus is now in use in over 300 other laboratories. Over 100 visitors from 38 states and 18 countries have published more than 300 scientific papers based on work done at the UCSF Computer Graphics Laboratory using MidasPlus and its predecessor MIDAS. Our current version of MidasPlus runs on the Silicon Graphics IRIS 4D and Indigo family of workstations, Digital Equipment DECstation 5000 and Alpha AXP workstations with the PXG or ZLX 3D graphics options, or any NeXT Computer workstation. Digital Equipment DECstation 5000 and Alpha AXP workstations require either a 24 bit ``true color'' PXG graphics option or the new ZLX graphics option to run MidasPlus. In order to obtain good image quality, a PXG graphics card should also be equipped with the optional Z buffer, although this is not strictly required. If performance is important for your work, the ZLX, PXG Turbo or Turbo+ graphics options offer the highest perfor- mance. MidasPlus does not run on VAXstations. Alpha AXP workstations require OSF/1 version 2.0 or greater and the optional OpenGL X server software. The DECstation 5000 version of MidasPlus is, unfortunately, in a transition state. The current version requires Ultrix 4.3 and Motif 1.1 and is implemented using the PEX server. PEX provides enough functionality for real-time line drawing images, but all of the other ``publication quality'' MidasPlus images are not available with PEX. At this time, it is not clear if DEC is going to support OpenGL on the DECstation 5000. Since our development plans call for converting MidasPlus entirely to OpenGL in the near future and since we feel MidasPlus without many of its key advanced features such as ``ribbon'' and ``conic'' images is of questionable valuable, we may soon decide to drop support of the DECstation 5000. Please direct all correspondence concering MidasPlus licensing to: Norma Belfer MidasPlus Distribution Coordinator Computer Graphics Laboratory University of California San Francisco, CA 94143-0446 Internet e-mail: norma %! at !% cgl.ucsf.edu. --->3 Squid From: Tom Oldfield yorvic.york.ac.uk> Squid will drive an X window device, but will only draw simple representations of space filling models. It does not generate space filling models using raster graphics or equivalent. Here is a standard replay... Computers The program is devoped on a Silicon graphics workstation, and is therefore most stable on this machine. It in continual use on SGI machines and there are very few fatal bugs. SQUID has been compiled and tested on other systems, and the code is designed to be portable (though not F77 standard). DEC Alpha AXP --- I have no access to these machines, so have not even tried compiling Squid on it. If you wish to try, it would be a great help. Note that you can run the program under X windows, or write you own graphics driver bases on the examples provided. Graphics SQUID is a graphics program that has the following device drivers:- Silicon graphics GL IBM GL Tektronix vt100 Sigma (not tested) postscript hpgl Xfig X windows If you do not have any of these then it is possible to write a new device driver in 100 lines of code as you only need ; start, stop, line, move. There is a routine called user_graphics.f that forms a blank device driver. Functions 1) Molecules.... a) Display - stick/ball&stick/ribbon/cpk/colour/stereo/labels/vectors b) Analysis - Dist/Ang/Tor/RMSD/weight/volume/planes/packing omega/chi(n)/phi/psi Statistics/DD-matrices/D-matrices Chirality/neighbours/ramachandran/H-bonds/2'struct/ Solvent-holes/isomerers/hyphobicity/etc 2) MD a) Display - atom/reduced/deviations/walks b) Analysis(time) - Rates of change/deviation/LSQ(time/atom/both) Covariance/Correlation/CA-matrix/ Dist/ang/tor/planes/Ranachandran/ Mean/SD/H-bonds/Packing/pairs/water/etc 3) Graphs a) 2D - Lines/hist/symbol/LSQ/dash/polar/curves/interpolation multiple/overlayed/labels/limits/templates/colour/gaussian b) 3D - Contour/isometric/tile/stack/ballon 4) Data processing All datasets (2D/3D graph, coordinates etc) can be *,/,+,- Functions can be applied..... trig/ln/log/exp/sqr/sqrt/abs/inverse/sort/average smooth/freq./PMF/stats./FFT/power/integral/ derivative/probability/boundaries 5) Database - Header database search - structure search - if supplied 6) Macro language a) Construct - for-endfor-step/if-endif/if-goto/if-break/nesting b) Variables - Any array value, users/logical/etc 7) Cluster analysis - Dendrograms(complete/single)/Graph theory/ Multidim' Scaling/adjancency/ 8) Drawing - pretty plots a) text - text/size/colour/orientation/groups/greek b) shapes - lines/points/arrows/boxs/circles/colour/style 9) Plotting - Get what you see always Postscript/HPGL/etc... See :- J.Mol.Graphics 1992 December Vol 10 pp 247-252 Getting a copy of the program Accademic institutions should mail me in reply to this message (oldfield (+ at +) yorvic.york.ac.uk). The program is available at no cost. Profit making organisations should get in touch with:- MSI 16 new Engalnd Executive Park Burlington MA 01803-5297 Tel 617 229 9800 Fax 617 229 9899 System requirements.... The code + documentation + data + junk = 7M bytes The program can be compiled with different parameter sets (squidparam.for), but the program as supplied runs in 6M bytes (5000 atom, 9*5000 2D point 3*200*200 3d grids etc....) Tom --->4 RasMol From: Bob Williams You can get RasMol from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. This is an X11 based system that has all of the features you mention, and it is free software. I have it running on my Alpha and am quite happy with it. From: albo %! at !% RUUCI9.chem.ruu.nl (Alexandre Bonvin) This might also be interesting: > >From: rasmol <-at-> dcs.ed.ac.uk (RasMol Molecular Graphics) >Subject: RasMol 2.2 Molecular Graphics Package Available >Keywords: RasMol, RasWin, molecular graphics >Date: 14 Oct 93 16:55:43 GMT > > RasMol 2.2 > Molecular Graphics Visualisation tool. > > Roger Sayle > Biocomputing Research Unit > University of Edinburgh > October 1993 > > This posting is to announce the public release of RasMol 2.2 molecular >graphics visualisation program. This package has been developed in the >BRU over the last few years, and the latest version has a significant >number of improvements over RasMol 2.1. These enhancements include protein >ribbon diagrams, secondary structure assignment (based on Kabsch and >Sander's DSSP algorithm), better amino acid classification, DNA hydrogen >bonding, DNA backbone representations, stick representations of hydrogen >bonds and disulphide bridges (either between backbone or sidechains), the >ability to write out selected atoms to a PDB file, support for Alchemy >format files, colouring of hbonds by their type, compressed PostScript >output, extended atom expression syntax, increased scroll bar functionality, >and many more additions (and bug fixes) too numerous to mention. For a >complete list of modifications (and acknowledgements), refer to the >distribution ChangeLog. > > RasMol is an X Window System tool intended for the visualisation of >proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) >files and interactively renders them in a variety of formats on either an >8bit or 24/32bit colour display. The complete source code and user >documentation for both the UNIX/X11 version and the IBM PC/MS Windows 3.1 >version may be obtained by anonymous ftp from ftp.dcs.ed.ac.uk >[129.215.160.5] in the directory /pub/rasmol. The UNIX/X11 source code is >contained in the file RasMol2.tar.Z and the MS Windows source code and >executable in the file raswin.zip. Both of these files include a slightly >dated version of the PostScript user reference manual. > > The program is intended for teaching and generating publication >quality images. The program has both a menu system and a full featured >command line interface. Different parts and representations of the >molecule may be coloured or displayed in a number of formats independently. >Currently supported formats include wireframe, ball and stick, backbone, >space filling spheres and protein ribbon models. The space filling spheres >may even be shadowed. The molecule may be manipulated using scroll bars, >the interactive command line or from a dials box if attached. The resulting >image may be saved at any point in PostScript, GIF, PPM, Sun rasterfile or >Microsoft BMP formats. For more details see the RasMol user reference. >It was claimed at a recent conference to be the fastest available >uniprocessor program for drawing shadowed spacefilled molecules. On a >SparcStation it can shadow a 10,000 atom protein in less than 10 seconds. > > The current version of the program has been tested on sun3, sun4, sun386i, >hp9000, sequent, DEC alpha, IBM RS/6000 and SGI, DEC and E&S mips based >machines compiled under both gcc and the native compiler. The version for >Microsoft Windows requires version 7 of the Microsoft Optimizing C Compiler >and the Microsoft Software Development Kit (SDK). > > The source code is public domain and freely distributable provided that >the original author is suitably acknowledged. Any comments, suggestions or >questions about the package may be directed to "rasmol -8 at 8- dcs.ed.ac.uk". > >Roger Sayle JANET: ros (+ at +) uk.ac.ed.dcs >Department of Computer Science UUCP: ..!mcsun!uknet!dcs!ros >University of Edinburgh ARPA: ros%dcs.ed.ac.uk(-(at)-)nsfnet-relay.ac.uk >Edinburgh EH9 3JZ, UK. Tel: (+44) 031 650 5163 (direct line) =========================================================================== | Alexandre Bonvin Ph.D. | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533859 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | CH 3584 Utrecht, The Netherlands | Email: albo -x- at -x- nmr.chem.ruu.nl | =========================================================================== --->5 mdXvu From: burkhart $#at#$ goodyear.com (Craig W. Burkhart) To: chemistry-: at :-ccl.net If you are interested in animating/property analysis, I believe there is a program from QCPE called mdXvu (QCPE #627). It is written for a pure X-windows environment, so it should be pretty portable. Check with them. Their salient info is: Quantum Chemistry Program Exchange Fone: 812.855.4784 Fax: .5539 Email: qcpe (- at -) ucs.indiana.edu ftp: qcpe6.chem.indiana.edu (anonymous ftp passwd: guest) P.S. mdXvu is written to deal with AMBER trajectory files. You can either input in this format, or write a routine to read your own custom trajectory files. -------------------------------------------------------------------------- Craig W. Burkhart, Ph.D. Senior Research Chemist E-mail: cburkhart -AatT- goodyear.com The Goodyear Tire & Rubber Co. Fone: 216.796.3163 Research Center Fax: 216.796.3304 142 Goodyear Boulevard Akron, OH 44305 --->6 Molpic From: loh %-% at %-% akocoa.enet.dec.com One of our collaborators is Steve Thompson at Cornell U, Dept. of Chemical Engineering. He has written a molecular graphics code called Molpic that works on Alpha AXP systems - he uses it to display molecular dynamics results for the materials problems he and Paulette Clancy solve. Steve IS distributing a version by FTP - so I recommend that you contact him at olin-0at0-cheme.cornell.edu. Molpic does indeed to space filling models, with very nice shading. It handles the requisite number of atoms. Steve has made movies of these via the multiple frames route. Let me know how you find it. Regards, Angela Molecular Sciences Marketing Manager Education/Research Marketing Group Digital ---> comment: Looks like pretty good software. The graphics routines can be called from C or fortran by linking to the libraries provided. Unfortunately, to make use of the full graphics capabilities, 24-bit color with PEX support is required. Our workstation has only 8 bit color. --->7 AVS Chemistry Viewer From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" You did not say what graphics you had on that machine. If you have a Denali head (graphics subsystem from Kubota or DEC) then the AVS Chemistry Viewer would be a good choice, especially at $500 academic pricing. If you do not have the Denali graphics, let me know what you do have and I can tell you if/when that hardware will be supported by the AVS Chemistry Viewer. Stop by the DEC booth at the San Diego ACS meeting to see the Chem Viewer in action. Douglas A. Smith, Ph.D. President The DASGroup, Inc. voice: 419-537-2116 or 419-472-9160 fax: 419-472-4757 email: dsmith.,at,.uoft02.utoledo.edu --->comment: I believe the extra graphics capabilities cost in the range of $5000-10000. We don't have them.