Software Distribution at SDSC
Lynn F. Ten Eyck
teneyckl at sdsc.edu
Wed Feb 9 17:38:31 EST 1994
Revision Date: February 9, 1994
The Computational Center for Macromolecular Structure (CCMS) is
distributing and supporting software for the determination and analysis
of the structures of biological macromolecules. CCMS is a joint
project of UCSD, The Scripps Research Institute, and the San Diego
Supercomputer Center, supported by the National Science Foundation.
Software is distributed and supported through the San Diego
ABSTRACT OF SOFTWARE
XTALVIEW is a package for X-ray crystal structure
solution from the point at which data is collected through the
fitting of a molecular model into an electron density map.
XtalView runs on ordinary workstations and DOES NOT REQUIRE 3-D
SHAPE is a package for analysis of molecular surfaces. It includes
programs for determining whether a point is in a groove or crevice
in a surface, and for determining the largest sphere that can fit
at a location.
FLEX is a simple display program that can show molecules and
animation sequences from disk files or from network connections to
running programs -- for example, a molecular dynamics simulation.
A library of communication routines is included which makes it very
simple to add this real-time display ability to any program.
All of our software is supported on the specified computer systems
(usually Sun, SGI, and DECstations; some runs on any Unix box). If you
find problems, we will attempt to fix them, and you may use the
consulting services of the San Diego Supercomputer Center for problems
with installation, documentation, or use of the software. This
includes e-mail (preferred) and telephone support. For help or
information by e-mail use the address ccms-help at sdsc.edu.
We will be using the e-mail addresses of our users to send them
about new versions and bug fixes as part of our support services. Our
mailing list will not be used for purposes other than support of our
All of our software is free for non-profit research use, but some of it
does require a license. Licenses are available from an e-mail list
server; specific conditions vary with the package, but generally are
not unduly restrictive. Any differences in terms for for-profit users
are noted under the specific packages.
We have different levels of access from the Internet corresponding to
different licensing requirements. Some software (e.g. FLEX) is freely
available without license by anonymous FTP.
Licensed packages require that we receive a signed license, but in the
interests of speed we will accept FAX versions of the license. Once we
have the license we will send access instructions by e-mail.
We are trying to measure the effect of our efforts to distribute some
of our packages, so those, while freely available, do require you to
send us your e-mail address. To obtain those packages you send an
e-mail request to ccms-request at sdsc.edu and the list server will return
access instructions for use with FTP, Gopher, or Mosaic. This should
cause very little delay in your obtaining the software. Since we are
trying to track the utilization of our software we request that people
who want copies be told how to get them directly from us rather than
simply being given copies or given the access information from other
sources. Our ability to continue this service will depend on our being
able to show those who pay the bills that we are performing a useful
service distributing portable, supported software.
Although electronic access is the preferred method for obtaining the
software, we will send tapes or floppy disks for those who cannot use
our electronic services. If you need a distribution in this form,
please either send e-mail to ccms-help at sdsc.edu or telephone our User
Services consultant, Ken Steube at (619)534-8311 or Jane Kwon at SDSC,
The following software is distributed currently:
XtalView is a complete package for solving a macromolecular crystal
structure by isomorphous replacement, including building the
molecular model. It runs on Sun, DEC, and SGI computers and takes
full advantage of the modern workstation environment. It has a
simple but comprehensive windows based interface. XtalView
maintains log files of the computations done. Standard file
formats are used, which facilitates communication between XtalView
and programs such as X-PLOR, TNT, and MERLOT.
XtalView is described in the book 'Practical Protein
Crystallography' by Duncan McRee, who also designed the program.
XtalView is free for non-profit use. For-profit users should
contact Duncan McRee (dem at scripps.edu, Telephone (619) 554-9235)
concerning licensing. A binary distribution is available
through the e-mail responder; source code is available, but
requires a signed license.
To receive information on obtaining XtalView software, send e-mail
ccms-request at sdsc.edu
leave the SUBJECT line blank
type ' get xtalview ' in the message
This is an automated process, and you'll receive instructions on
how to get a copy of the XtalView binaries and also a license
agreement form for the source code of XtalView by return e-mail.
We ask that you return the signed license agreement if you'd
like to receive the source code of XtalView ( ~100000 lines of C
and Fortran ).
Analysis tools for solvent-accessible molecular surfaces, including
Surfractal, which calculates the local fractal dimension to define
grooves and protrusions on surfaces, MaxAccess, which determines
the radius of the largest sphere accessible to each surface point,
and SrftoBiosym, which bins and converts surface file output into
Shape is licensed by The Scripps Research Institute. This software
may be obtained by e-mail request. We ask that you return a signed
copy of the software license agreement sent in response to your
To receive information on obtaining SHAPE software, send e-mail
ccms-request at sdsc.edu
leave the SUBJECT line blank
type ' get shape ' in the message
This is an automated process, and you'll receive a copy of the
license agreement and instructions on how to get a copy of the
software by return e-mail.
Flex is a simple, portable molecular graphics program that
interactively displays 3D ball-and-stick models on workstations
running the Xwindows system. Flex can accept input read from a
file or passed over a network socket connection. The latter
functionality makes flex ideal for monitoring large-scale
simulations as they progress. Flex provides a library of
subroutines, netg, to support this function. There are other
(earlier) versions of Flex available on the net; this one is
supported and includes documentation of the communications library.
Flex is accompanied by ffe (flex front end), a program that
connects to flex over a socket and allows more precise user control
of the displayed molecule.
Flex is freely available by anonymous FTP at ftp.sdsc.edu in the
directory pub/ccms/flex. The README file in that directory
contains most if not all of the information you will need. If you
have other questions or comments, send e-mail to
ccms-help at sdsc.edu
More information about the Bio-soft