CALL FOR DISCUSSION: X-PLOR/bionet.software.x-plor

BIOSCI Administrator biosci-help at net.bio.net
Mon Apr 24 19:58:41 EST 1995


We have received a proposal below for a new newsgroup,

X-PLOR/bionet.software.x-plor

This group is currently a BIOSCI prototype newsgroup, so it must
either pass successfully through the voting process or be shut down.

Discussion on the following proposal will now be open through 4 May
on BIOFORUM/bionet.general (*not* on BIONEWS/bionet.announce).  For
those who are not on the BIOFORUM/bionet.general newsgroup currently,
either read bionet.general on USENET or contact one of the following
biosci addresses to sign up by e-mail:

Subscription Address                 Location
--------------------                 --------
biosci at daresbury.ac.uk               Europe, Africa, and Central Asia
biosci at net.bio.net                   Americas and the Pacific Rim

One warning, however: BIOFORUM/bionet.general is a "chatty" newsgroup
and many other items will be discussed there besides this newsgroup
proposal.  USENET news access is definitely better than e-mail if you
want to monitor only this discussion.

Discussion Guidelines
---------------------
Please do not post one-line messages saying things like "I am in favor
of such a newsgroup".  We will collect votes later.  The discussion
period is an opportunity for anyone to bring up reservations about the
proposed charter below and to propose modifications prior to the vote.
If the charter is perfect as is, then there is no need for anyone to
say anything!!!

The newsgroup discussion leader may submit a revised proposal in light
of the discussion, and the new charter would be included in the call
for votes which will go out on 5 May (Newsgroup Discussion leaders -
please note this deadline - if no revisions are received before the
deadline, the original charter will be voted on.).

Please be aware that only one vote is counted per e-mail address, so
it is necessary to have your own account in order to vote.  Multiple
votes from the same address are not accepted.  If you are interested
in the following newsgroup, but do not have an e-mail address of your
own, please obtain one from your computer center before the call for
votes is issued.

---------------------------------------------------------------------
Proposal to establish X-PLOR/bionet.software.x-plor

Proposed USENET name: bionet.software.x-plor

Proposed mailing list name: X-PLOR

Proposed mailing addresses: x-plor at net.bio.net
                            x-plor at daresbury.ac.uk

Discussion leader:

Axel T. Brunger
Howard Hughes Medical Institute and
Dept. of Molecular Biophysics and Biochemistry
Yale University
P.O. Box 208114
266 Whitney Avenue
Bass Center for Molecular and Structural Biology (BCMSB)
New Haven
CT 06520-8114

PHONE number: (203)-432-6143
FAX number: (203)-432-6946
Internet:  brunger at laplace.csb.yale.edu


Newsgroup charter:

X-PLOR is a forum for all those interested in using the program X-PLOR
for three dimensional structure determination of macromolecules using
X-ray Crystallography and Nuclear Magnetic Resonance Spectroscopy
(NMR).  X-PLOR is a program system for computational structural
biology. X-PLOR stands for exploration of conformational space of
macromolecules restrained to regions allowed by combinations of
empirical energy functions and experimental data.  But it also stands
for exploration of modern concepts of structured programming in
macromolecular simulation.

X-PLOR's main focus is the three-dimensional structure determination
of macromolecules using crystallographic diffraction or nuclear
magnetic resonance (NMR) data. The program is based on an energy
function approach: arbitrary combinations of empirical, geometric and
effective energy terms describing experimental data may be used. The
combined energy function can be minimized by a variety of gradient
descent, simulated annealing, and conformational search procedures.
X-PLOR was the first program to combine X-ray crystallographic
diffraction data and molecular dynamics for refinement. Since then the
program has undergone extensive development, and the focus has shifted
from refinement to structure determination. Major features of
computational X-ray crystallography and solution NMR-spectroscopy have
been included. Ongoing development of X-PLOR is aimed at providing a
comprehensive system for all computational aspects of macromolecular
structure determination.  A new release of the program is scheduled
for late 1995.

X-PLOR is more than a program: it is a macromolecular language. This
flexible language allows the user to experiment with new ideas without
being restricted to standard or hard-wired protocols. X-PLOR was
designed to provide user friendliness, machine portability, and highly
efficient algorithms for modern computers.

The program has been implemented on nearly all modern computer types
including vectorizing supercomputers. Furthermore, planning for a
general parallel version of X-PLOR has begun. Since the program has
been written in standard FORTRAN-77, it is usually straightforward to
implement the program on a new machine.  X-PLOR is currently used by
several thousand researchers in over 800 laboratories worldwide.

I propose the formation of a newsgroup called
"X-PLOR/bionet.software.x-plor" to continue dialogue between
scientists whose interests comprise the following:

*** reports of new developments and applications with X-PLOR

*** posting of frequently-asked questions and answers

*** reports of bugs and work-arounds

*** interchange of ideas for using X-PLOR

*** general discussion of issues relating to computational crystallography and
    solution NMR


Formation of a newsgroup will provide:

*** a forum for discussion of new ideas and recent developments for future
    versions of X-PLOR

*** a source of information for both novice and experienced participants.

*** bulletin board for announcements of bugs and new features.

*** means for initiating collaboration among participants.

*** a repository of practical advice and other information, including advances
    in relevant methodology.

The newsgroup will be unmoderated.
----------------------------------------------------------------------



More information about the Bionews mailing list