From SATYAM@vms.cis.pitt.edu Wed Feb 16 11:36:37 1994 Received: from VM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.4/930601.1506) id LAA18929; Wed, 16 Feb 1994 11:07:31 -0500 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF #12376) id <01H8Y91ATHV490QHOK@vms.cis.pitt.edu>; Wed, 16 Feb 1994 11:05 EST Date: Wed, 16 Feb 1994 11:05 EST Subject: Redox Potentials for Amino-acids.. To: chemistry@ccl.net Message-id: <01H8Y91ATHV490QHOK@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netter, Where can one find the redox potentials of amino acids.. pointers to author/articles will be helpful. I had a look at handbook of electrochemistry by Meites et.al on orgranic and inorganic chemistry. Thanks in advance satyam From toni@athe.WUstl.EDU Wed Feb 16 13:25:38 1994 Received: from wugate.wustl.edu for toni@athe.WUstl.EDU by www.ccl.net (8.6.4/930601.1506) id MAA00366; Wed, 16 Feb 1994 12:33:27 -0500 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA26588; Wed, 16 Feb 1994 11:32:49 -0600 Received: by athe.WUstl.EDU (4.1/SunOS 4.1.1); Wed, 16 Feb 94 11:32:47 CST Date: Wed, 16 Feb 94 11:32:47 CST From: toni@athe.WUstl.EDU (Toni Kazic) Message-Id: <9402161732.AA16199@athe.WUstl.EDU> To: chemistry@ccl.net Subject: Electronic publishing on the World Wide Web Cc: hunter@nlm.nih.gov, kcross@cas.org Dear Netters, Recently someone asked if a form for electronic submission of ACS abstracts existed. The question came up during the recent discussion of the potential of electronic publishing, and the uses to which the World Wide Web might be put. It seemed to me a natural opportunity to use the former to illustrate the latter. Kevin Cross of the ACS was kind enough to send me a copy of the official submission form. Hugh Chou and I have built a Mosaic window which collects the information on the form, including the text and figures for the abstract, and assembles the abstract automatically. THIS DOESN'T SUBMIT THE ABSTRACT TO THE ACS; it's merely to demonstrate the possibilities. The result can be viewed by clicking the appropriate highlighted text anchors. The information is collected and processed via a Perl script; a LaTeX file is generated; and the PostScript output is displayed via whatever viewer your Mosaic client uses. We did not attempt to actually collect the data in the boxes, apart from that immediately relevant to the abstract, since we don't know what the ACS does with it: but the possibilities for automated abstract tracking and meeting management are obvious. You can access the window from http://ibc.wustl.edu/acs/acs_form2.html The LaTeX style file (acs_abstract.sty) and a sample LaTeX abstract (acs.tex) are available for "home use". The Perl scripts which form the back end (page1.perl, page2.perl, and get_url.perl) are also there. The HTML code for the form proper can be pulled directly from the Mosaic window by hitting the "View Source" button under "File" at the top menu bar. Everything is free to the public, of course. Those who followed the recent discussion on programming languages and paradigms may find our multilingual approach interesting. Please try this out and let us know what you think. Toni Kazic Institute for Biomedical Computing Box 8036 Washington University School of Medicine 700 South Euclid Ave. St. Louis MO 63110 314-362-3121 314-362-0234 (fax) toni@athe.wustl.edu From jxh@ibm12.biosym.com Wed Feb 16 14:28:41 1994 Received: from ibm12.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.4/930601.1506) id NAA01524; Wed, 16 Feb 1994 13:28:41 -0500 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA17850; Wed, 16 Feb 1994 10:28:12 -0800 Date: Wed, 16 Feb 1994 10:28:12 -0800 From: jxh@ibm12.biosym.com (Joerg Hill) Message-Id: <9402161828.AA17850@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: Point group determination by a programme Since there is obviously an interest in learning something about how to determine point groups with a computer programme here my DM 0.034 (=$0.02): All physical properties of a molecule have to be invariant to the application of a symmetry operation. If we consider an easy to calculate property such as the inertia tensor of the molecule we see first that all symmetry elements must pass the centre of gravity. If we diagonalize the inertia tensor we get three moments of inertia (eigenvalues) and three principal axes of inertia (eigenvectors). Now we can distinguish some cases: 1) one moment of inertia is zero, the others not --> the molecule is linear, possible point groups C*v or D*h (the * stands for infinite), check by comparing the atoms 2) all three moments of inertia are different (asymmetric top molecules) --> no axes of order greater than 2 are possible, point groups D2h, D2, C2v, C2h, C2, Ci, Cs, and C1, if at least one of the principal axes is C2 you have either D2h (all principal axes are C2 and an inverson centre exists), D2 (as D2h, but no inverson centre), C2v, C2h, or C2; otherwise you have Ci, Cs, or C1. 3) two moments of inertia are the same, the third is different (symmetric top molecules) --> all axial point groups except the cubic ones (T, Td, Th, O, Oh, I, Ih) are possible, your unique principal axis of inertia is one rotation axis and you can further distinguish by comparing sets of atoms. 4) all three moments of inertia are the same (spherical top molecules) --> possible point groups T, Td, Th, O, Oh, I, Ih and you have a problem ! It is not possible to obtain a rotation axis from the inertia tensor (where is top or bottom of a sphere ?) But you can check sets of atoms. Since each symmetry element has to pass through the centre of gravity you can calculate the distance atom from the centre of gravity and if you find a set of atoms of the same element with the same distances from the centre of gravity you have found a rotation axis. Note: There are a few cases of so-called accidiental spherical top molecules which do not belong to a cubic point group. These are hard to handle, but rare, too. OK, that's the basic algorithm. Literature for this is rare. Most textbooks only deal with symmetry operations, point groups etc., but not with how to get this into a running programme. I only remember an anchient spectroscopy textbook, which explained somewhat of this algorithm, but I can't cite it. Available codes are basically Turbomole, which uses all this stuff to speed up calculations, since you can reduce the computional effort by the order of the point group. Joerg-R. Hill From rgab@purisima.molres.org Wed Feb 16 18:24:54 1994 Received: from purisima.molres.org for rgab@purisima.molres.org by www.ccl.net (8.6.4/930601.1506) id RAA07196; Wed, 16 Feb 1994 17:36:17 -0500 Message-Id: <199402162236.RAA07196@www.ccl.net> Received: by purisima.molres.org (1.37.109.4/16.2) id AA15320; Wed, 16 Feb 94 14:38:40 -0800 Date: Wed, 16 Feb 94 14:38:40 -0800 From: "R.G.A.Bone" To: chemistry@ccl.net Subject: determining point groups Concerning the various perspectives on deducing the geometric symmetry of a molecule from its nuclear coordinates: i) The Gaussian package readily does this, (one of its more irritating features I should add), though you can turn symmetry off with a whole manner of flags at the various levels of calculation, you know, dep- ending on how you want to "fix" your result (cf. 'symmetry-broken' solutions in UHF). ii) Philosophically (regrettably) given that assemblies of nuclei (i.e., molecules) are not static - there are continuous vibrations, etc., the only molecules which will have any geometric symmetry at all, at any instant, are triatomics (a plane of symmetry) and diatomics. The latter will have the infinite-fold rotation axis (and a whole "bunch" of others if homonuclear). Thus, only if two nuclei have symmetry-related coordinates (to some arbitrary level of precision) is geometric symmetry present. Of course, one could specify this level of precision to be the dimension of a nucleus (typically femtometres). But, being chemists, with an under- standing of spectroscopy, we know a little better and assume that, for all intents and purposes point-symmetry operations commute with the vibronic Hamiltonian so this issue does not arise and the 'time-averaged' position of the nuclei, or the geometry at the well in the potential is what counts. iii) But, if you are a computer, to examine a number of nuclear coordinates and determine symmetric-relationships between them requires some intell igent decision concerning what is "near-symmetry" and what is "exact- symmetry". Suppose there are small rounding errors in the data: e.g., 2 nuclear positions: 1.00000000 0.50000000 2.34567890 1.00000000 0.50000000 -2.34567889 Are these 2 nuclei symmetrically-related? Well, surely yes, although their z-coordinates differ by a trivial amount. The algorithm must contain a threshold-cutoff which copes with cases like this. iv) In response to the comment that you need to know the nuclear identity as well as the coordinates in order to deduce symmetry. Well, except for the trivial case of diatomics, I challenge anybody to find 2 nuclei in a molecule which are NOT identical but which are in exactly-symmetry- related coordinates, to say 10^-6 Angstrom precision. Of course, there may be circumstances under which it is desirable to label (for example iso- topic) substituents as symmetrically-equivalent, and cases where it is not. But that's moving the goal-posts. It also depends on the source of the data: is it an experimental or theoretical geometry for the isotopomer? (i.e., have zero-point effects been included or not ?) Basically, this matter of deducing the point group from a set of coordinates does have a slight algorithmic difficulty, which is perhaps why it has not been widely implemented. Arguably also, let's face it: almost all molecules on this planet don't have any symmetry at all; (theoretical) chemists' obsession with symmetry comes from 1) the small size of molecules they are accustomed to dealing with (symmetry is more preponderent in small molecules), 2) the fact that, even for small molecules, use of symmetry can make a big calculation more practical. Furthermore, there are hardly any molecules for which the point group can't be deduced "by inspection", unless there happens to be a potential confusion between "near-symmetry" and actual-symmetry. One might argue that that difficulty increases as molecules increase in size, but then the amount of symmetry typically decreases in the same way (crystal-lattice unit-cells, excepted). Richard Bone ================================================================================ R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org ------------------------------------------------------------------------------- --------------------- Every Theory has its "Grassy Knoll" --------------------- ------------------------------------------------------------------------------- From faeder@jila02.Colorado.EDU Wed Feb 16 18:32:05 1994 Received: from jila02.Colorado.EDU for faeder@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@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@jila02.Colorado.EDU> To: chemistry@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@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@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@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@cgl.ucsf.edu. --->3 Squid From: Tom Oldfield 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@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@RUUCI9.chem.ruu.nl (Alexandre Bonvin) This might also be interesting: > >From: rasmol@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@dcs.ed.ac.uk". > >Roger Sayle JANET: ros@uk.ac.ed.dcs >Department of Computer Science UUCP: ..!mcsun!uknet!dcs!ros >University of Edinburgh ARPA: ros%dcs.ed.ac.uk@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@nmr.chem.ruu.nl | =========================================================================== --->5 mdXvu From: burkhart@goodyear.com (Craig W. Burkhart) To: chemistry@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@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@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@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@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@uoft02.utoledo.edu --->comment: I believe the extra graphics capabilities cost in the range of $5000-10000. We don't have them. From mw@crystal.uwa.edu.au Wed Feb 16 23:25:28 1994 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.6.4/930601.1506) id WAA09135; Wed, 16 Feb 1994 22:56:31 -0500 Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.6.4/8.6.4) with SMTP id LAA29165 for ; Thu, 17 Feb 1994 11:56:21 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA19183; Thu, 17 Feb 1994 12:38:14 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9402170345.AA14827@pack.crystal.uwa.edu.au> Subject: Dr. Shreeve's address? To: chemistry@ccl.net Date: Thu, 17 Feb 94 11:45:52 WST Mailer: Elm [revision: 70.85] Dear Netters, I know we not suppose to ask for email address, but I have been trying to find the email address of Dr. Shreeve everywhere and no luck. Maybe someone knows how to get in contact with him. Thank you very much for your help. Magda Wajrak (mw@crystal.uwa.edu.au) From peschko@mermaid.micro.umn.edu Wed Feb 16 23:39:21 1994 Received: from mermaid.micro.umn.edu for peschko@mermaid.micro.umn.edu by www.ccl.net (8.6.4/930601.1506) id WAA09112; Wed, 16 Feb 1994 22:48:32 -0500 Received: from stingray.micro.umn.edu by mermaid.micro.umn.edu (5.65c/Tony Tiger 1.34) id AA17260; Wed, 16 Feb 1994 21:48:25 -0600 From: peschko@mermaid.micro.umn.edu (Edward Peschko) Message-Id: <199402170348.AA17260@mermaid.micro.umn.edu> Subject: Need code for Sim. Annealing algorithm test To: CHEMISTRY@ccl.net Date: Wed, 16 Feb 94 21:48:25 CST X-Mailer: ELM [version 2.3 PL11] hey all -- I have developed a new variant of simulated annealing, and wanted to test it out on the protein folding problem. Unfortunately, I know more about programming sim. annealing than I do programming molecular pot. energy packages. So: I was wondering if there was any public domain packages out there that could do the following (and that I could test my code with): (And barring public domain, some non-public domain stuff) 1)Figure out a 'good' protein structure based on the bond lengths/angles inherent in that structure... 2) Figure out the approx potential energy of a given polypeptide chain given the 3D coordinates of the alpha carbons, or the phi,psi angles -- and possibly add sidechains as well. I am aware of CHARMm, GROMOS and Discover, and would also like to get a sense of their limitations as well as their strengths. Thanks much, Ed (PS: I apologize to all those on the Insight/Discover list for this, which is a cross-posting)