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Education Sampler 1992 [NeXTSTEP]
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Education_1992_Sampler.iso
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Chemistry
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Midas
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README
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1992-08-21
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MidasPlus - Molecular Interactive Display and Simulation System
Computer Graphics Laboratory
University of California, San Francisco
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 "publication quality" space filling
images with multiple light sources and shadows. 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. Complex
inorganic compounds and large polymers with many crosslinks are
handled ungracefully. See the MidasPlus User's Manual for full
details.
MidasPlus was initially developed in the early 1980's, and until
recently has run only on high performance interactive graphics
workstations such as the Silicon Graphics IRIS. Versions are now
available the NeXT family of workstations, the SGI IRIS family of
workstations, and the DECstation 5000 PXG family of workstations.
Because of the lack of full support for doing three dimensional
image rotations and translations using the NeXTDIMENSION graphics
option prior to NeXTSTEP 3.0, the current version of MidasPlus for
the NeXT can effectively handle only small proteins, nucleic acids
and drug models. A color system is essential for serious modeling
work, although the software is capable of running on a black and
white NeXTSTATION as well. As with most workstations, the more
main memory you have the better the application will perform; we
consider 20MB on a color NeXTSTATION and 32MB on a NeXTDIMENSION
system to be adequate. If you plan to work with many models, 400MB
of disk should be considered an absolute minimum.
If you are interested in reading more about MidasPlus three good
references are:
1. T.E. Ferrin, C.C. Huang, L.E. Jarvis, and R. Langridge,
"The MIDAS Display System," J. Mol. Graphics, 6(1):13-
27,36-37, 1988.
2. T.E. Ferrin, G.S. Couch, C.C. Huang, E.F. Pettersen, and R.
Langridge, "An Affordable Approach to Interactive Desktop
Molecular Modeling," J. Mol. Graphics, 9(1):27-32,37-38,
1991.
3. "The Coming of Desktop Molecular Modeling", NeXT on Campus,
2(3):8-9, Spring 1991.
If you'd like to see some recent sample MidasPlus images created
on a Silicon Graphics IRIS system, some good examples can be found
in:
1. A.M. De Vos, M. Ultsch and A.A. Kossiakoff, "Human Growth
Hormone and Extracellular Domain of Its Receptor: Crystal
Structure of the Complex", Science, 255(5042):cover and
306-312, 1992.
The distribution of MidasPlus included on this "NeXT Public Domain
CD-ROM for Education" is a binary-only version of the system. It
has been tested extensively under NeXTSTEP release 2.1 and in a
much more limited fashion under NeXTSTEP 3.0 beta pre-release 2.
This version does NOT use Interactive RenderMan (IRM), and hence does
not take advantage of the high performance 3D graphics available with
the NeXTDIMENSION option under release 3.0.
MIDASPLUS IS COPYRIGHTED BY THE REGENTS OF THE UNIVERSITY OF CALIFORNIA.
THE BINARY-ONLY VERSION OF MIDASPLUS INCLUDED ON THIS CD-ROM IS LICENSED
ON A PER WORKSTATION BASIS FOR $99 PER COPY. A ONE WEEK "DEMO LICENSE"
IS AVAILABLE FREE OF CHARGE. SEE BELOW FOR DETAILS ON NOW TO OBTAIN
THE LICENSE PASSWORD NECESSARY FOR ACTIVATING THE MIDASPLUS APPLICATION.
You must install MidasPlus on your hard disk in order to use it. The
MidasPlus application and assorted support programs take approximately
2 MB of disk space and reside in the directories /LocalApps, /LocalLibrary,
and /usr/local/{bin,lib,man}. Use the standard NeXT Installer application
to do the installation. You do not need to install the compressed PostScript
documentation if you just want to print it. If you want the MidasPlus
manual pages to be seen by the Digital Librarian and the UNIX "man" command,
you will need to make a couple of symbolic links after you have run the
Installer App.. On a NeXTSTEP 2.{0,1,2} system do (as root):
ln -s /usr/local/man/manl /NextLibrary/Documentation/Unix/ManPages/manl
and
ln -s /usr/local/man/catl /NextLibrary/Documentation/Unix/ManPages/catl
On a NeXTSTEP 3.0 system do:
ln -s /usr/local/man/manl /NextLibrary/Documentation/ManPages/manl
and
ln -s /usr/local/man/catl /NextLibrary/Documentation/ManPages/catl
The binary-only distribution of MidasPlus contains no source code
and no printed documentation, but otherwise is a fully functional
release. PostScript versions of the MidasPlus User's Manual
(manual.ps.Z), MidasPlus Command Quick Reference Card (quickref.ps.Z),
and Version 1.8 Release Notes (release-notes.ps.Z) are included in
this directory. The manual is 130 pages in length and fully documents
the MidasPlus system. Serious users are encouraged to print out the
manual and study it carefully to determine the many features and
limitations of the system. A "show and tell" style introduction to
MidasPlus can be found in the "Demos" directory. Additional demos
can be found in Demos/{dna,crodna} and a PDB model of the protein
Glucagon can be found in /LocalLibrary/Mol/pdb. See the individual
"README" files in each of the subdirectories for demo operating
instructions.
MidasPlus is also licensed in source form to universities and other
organizations. The license fee is $350, which includes complete
source code, distribution media, machine readable and printed
documentation, and our administrative overhead costs. Support and
training are not available, although we do welcome bug reports and
periodically issue update releases that incorporate bug fixes.
Please note that we are an academic institution with limited personnel
and not a commercial software company.
To obtain either a free one week demo license or a $99 per workstation
binary-only license for the MidasPlus software system, do the following:
1. Install the MidasPlus package on your NeXT workstation
hard disk by double-clicking on the Midas.pkg icon.
2. Start up MidasPlus by double-clicking on the /LocalApps/Midas
icon. A alert panel will pop up showing the unique machine
identifier for your workstation.
3. Send an email message to midas-license@cgl.ucsf.edu (Internet),
or send US mail to the address shown below, or call 415-476-5128
and ask to speak with the MidasPlus license coordinator. You
must supply the following information:
a) Name
b) Title
c) Instutional affiliation
d) Address
e) Phone number
f) Machine identifier
g) A check or purchase order for $99 (optional).
4. A 16 digit license password will be returned to you. Add
this password along with your machine identifier to the list
of passwords in /LocalLibrary/Midas/demo_passwords and then
double-click on the /LocalApps/Midas icon.
5. In order to run the overview demo on a 3.0 system, or to be
able to double-click on files with .pdb extensions, you will
either need to logout and log back in again, or wait until
the workspace manager discovers MidasPlus has been installed.
License requests which do not include a check or purchase order will
receive a one-week license free of charge (one time only). Requests
with include payment will receive a license password good for ten years.
If your payment is via a purchase order, it will take time for the
purchase order to be processed before your license is issued (some
institutions and government agencies are very slow in paying, so you
may wish to consider paying by check in order to avoid potential delays).
Our US mail address is:
MIDAS Software Distribution
c/o Norma Belfer
Computer Graphics Laboratory
School of Pharmacy
University of California
San Francisco, CA 94143-0446
Institutions interested in licensing MidasPlus in source form (source
license are NOT available to individuals) should send an email inquiry
to midas-license@cgl.ucsf.edu (Internet). A license agreement will be
sent to you which must be signed by your legal department and returned
with payment or purchase order. Distribution media is floppy disk.
We hope you will find MidasPlus as useful in your research as we do.
Well over 200 scientific publications have resulted from work at the
UCSF Computer Graphics Laboratory using MidasPlus. The software is
actively used in research labs throughout the USA and many foreign
countries.
MidasPlus was developed at the UCSF Computer Graphics Laboratory
through support from the University of California and the National
Institutes of Health National Center for Research Resources (NCRR
grant RR-01081, Robert Langridge principal investigator). Conrad
Huang, Greg Couch, Eric Pettersen and Tom Ferrin are the principal
authors of the MidasPlus software package.
--Tom Ferrin
16-Aug-92