XtalView 3.1b Software for Macromolecular Crystallography

Lynn Ten Eyck teneyckl at aurora.sdsc.edu
Thu Mar 28 22:24:43 EST 1996


XtalView 3.1 is overdue for a major workout by interested
crystallographers and molecular modelers.  The new version includes
major enhancements to electron density fitting, and a number of bug
fixes on the DEC Alpha version, as well as minor bug fixes elsewhere.
Naturally we think this release is fine . . . but since we are
changing the way it is packaged, and because this release has not been
widely used outside our own groups yet, we are calling it a beta
release.

If you are impatient, just go to http://www.sdsc.edu/CCMS -- otherwise
read on for the sales pitch, which is an abridged version of the
Release Notes.

Lynn Ten Eyck
teneyckl at sdsc.edu

*************************************************************************
*      The Computational Center for Macromolecular Structure (CCMS)     *
*************************************************************************
*                             X t a l V i e w                           *
*                             Release 3.1beta                           *
*                                                                       *
*        (C) The Scripps Research Institute and Duncan E. McRee         *
*                       10666 N. Torrey Pines Rd.                       *
*                          La Jolla, CA 92037                           *
*                                                                       *
*     Author:         Duncan E. McRee, TSRI                             *
*     Contributors:   Alex Shah, Andy Arvai, Mike Pique, & Mark Israel  *
*************************************************************************
Platform Info
-------------
Initial support for XtalView 3.1beta includes the following platforms:

	SunOS4
	SunOS5
	IRIX 5
	IRIX64
	OSF/1 V2 and V3 (versions use same executables)
	IBM RS/6000

The source is known to compile on other platforms, but archives of the
executables may not yet be available (for RS/6000, Linux, IRIX4).

XtalView compiles and runs as 32-bit executable on IRIX64. There are some
problems with running the IRIX5.2 executables on IRIX64 systems, so CCMS
provides executables for IRIX64.

XtalView now uses shared xview libraries on the IRIX 5 and 6 and DEC Alpha
OSF/1 systems in addition to the Sun systems.

Previous distributions of XtalView used subdirectories named make_ARCHOSV
for each supported architecture. These are no longer required and are no
longer distributed with the programs.

Several DEC Alpha bugs have been fixed. These related to the 64-bit
pointer size. Several problems were fixed by adjusting the header
from the f2c translator.

xfit does not properly display on some DEC Alpha systems with 24-bit
color displays. We have seen two problems: the canvas gets drawn 
properly except for a severe flicker while rotating the molecule, 
and on other systems the canvas does not get drawn at all leaving a 
blank canvas.  These are believed to be related to a known bug in the
DEC Turbochannel X-server, which DEC is not going to fix.  It works
fine on most of the Alphas we have tried.

New Feature in Xheavy
---------------------

xheavy has a new input file to refine against:  specify a phase file
in the panel labeled "Input phases:" in the xheavy main window.

NEW FEATURES IN XFIT
--------------------
--------------------

Automatic fitting
-----------------

The major new features in xfit are to support semi-automated fitting 
of models to electron density.  A tutorial describing them, "Xfit 
Automated Fitting Features", is available on the World Wide Web at:

   <http://www.scripps.edu/pub/dem-web/tutorial/xfitauto.html>

A table of contents of other WWW documents is at:

   <http://www.scripps.edu/dem-web/toc.html>

Customization
-------------

xfit now accepts commands on startup from a file called ".xfitrc".

All the toggles and sliders in xfit are now available as script 
commands.  To get a complete list, simply make a script and look at 
the commands that are automatically included within.

Toolbar, mouse, dials
---------------------

General changes
---------------

Numerous changes to make the program more convenient and useful.
Check the Web site http://www.sdsc.edu/CCMS for more information.
-- 
Lynn F. Ten Eyck (teneyck at sdsc.edu)    Tel: (619) 534-8189
San Diego Supercomputer Center         FAX: (619) 534-8193
P.O. Box 85608
San Diego, CA 92186-9784




More information about the Bio-soft mailing list