Subject: Request for Molecular Graphics Software-- Summary

From: jim faeder <[email-masked]>
Date: Wed, 16 Feb 1994 16:03:23 -0700

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: [email-masked] (Jesus M. Castagnetto Mizuaray)
If you can output XYZ coordinates, maybe XMol it's for you. You can
get info from [email-masked]. 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-
    [email-masked]       | 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 <[email-masked]>
     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: [email-masked].

--->3 Squid
From: Tom Oldfield <[email-masked]>
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 ([email-masked]).  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 <[email-masked]>
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: [email-masked] (Alexandre Bonvin)
This might also be interesting:
>
>From: [email-masked] (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 "[email-masked]".
>
>Roger Sayle                        JANET: [email-masked]
>Department of Computer Science     UUCP:  ..!mcsun!uknet!dcs!ros
>University of Edinburgh            ARPA:  [email-masked]
>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: [email-masked] |
===========================================================================

--->5 mdXvu
From: [email-masked] (Craig W. Burkhart)
To: [email-masked]
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:    [email-masked]
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: [email-masked]             The Goodyear Tire & Rubber Co.
Fone:   216.796.3163                       Research Center
Fax:    216.796.3304                       142 Goodyear Boulevard
					   Akron, OH   44305
--->6 Molpic
From: [email-masked]
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 [email-masked]. 

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" <[email-masked]>
	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:	[email-masked]

--->comment:
I believe the extra graphics capabilities cost in the range of $5000-10000.
We don't have them.