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
Supercomputer Center.


    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.


    1.  SUPPORT 
    2.  LICENSING 
    3.  ACCESS 
    4.  PACKAGES


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
    Biosym-readable format.

    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

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