[3DEM] new release of 'Situs' hybrid modeling package

[David Foster]

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Message from Willy Wriggers forwarded to list by Moderator.

Dave Foster

-------- Original Message --------
Subject: 	new release of 'Situs' hybrid modeling package
Date: 	Wed, 19 Oct 2005 15:14:55 -0500
From: 	Willy Wriggers <willy.r.wriggers at uth.tmc.edu>
Organization: 	biomachina.org
To: 	3dem at ucsd.edu

Dear colleagues,

We are releasing a major update of our free Situs hybrid modeling
package, version 2.2, which is now online at http://situs.biomachina.org

Version 2.2 includes many significant improvements and added features
compared to the previous version. Here are the highlights (a more
detailed explanation is appended below):

     * support of parallel (multi-processor) computing for the popular
       /colores/ tool
     * improved peak search and angular sampling algorithms
     * integration with molecular graphics programs (VMD
       <http://www.ks.uiuc.edu/Research/vmd/>, SenSitus
       <http://sensitus.biomachina.org>)
     * FFTW library included in distribution, now portable to Windows
       (cygwin shell)
     * support of manual fitting and refinement of  visually docked
       structures
     * support of map-to-map fitting
     * improved editing, segmentation, difference mapping tools
     * support of flexible fitting using "motion capture" skeleton editing

As before, the package including source codes can be downloaded free of
charge, under the GNU General Public License.

Sincerely,

Jochen Heyd, Valerio Mariani, Paul Boyle, and Willy Wriggers (authors of
this update)

URL: http://situs.biomachina.org
Laboratories for Biocomputing & Imaging
School of Health Information Sciences & Institute of Molecular Medicine
University of Texas Health Science Center at Houston
7000 Fannin St., Suite 600
Houston, TX 77030
____________________________________________________________


*Detailed explanation of changes:*

     * The /colores/ 6D exhaustive search tool has been one of the main
       focal points of the current development. First, the execution
       times have been drastically reduced due to both algorithmic
       improvement and parallelization. The two most compute intensive
       parts of the program, the on-grid FFT based exhaustive search and
       the off-grid Powell optimization, can now take advantage of
       multiprocessor systems and multicore or hyperthreaded processors.
       The speedup is very close to the number processors or cores used
       for the calculation.  Second, the Powell optimization now has a
       choice of three different cross-correlation algorithms. The
       fastest accurate algorithm is chosen at runtime depending on the
       system under study. For many systems, speedups of 2-3 for the
       Powell optimization can be achieved. In extreme cases (for very
       small probe structures), speedups can be as high 2000.  Overall,
       these speed improvements add up to significant time savings. For
       example, the total execution time for the/ //colores/ tutorial is
       reduced from 8 to 3 minutes using Situs 2.2.

     * The present version of /colores/ also uses a new peak search
       algorithm by default.  Previous versions just sorted the list of
       peaks found by the exhaustive search and refined the top candidate
       peaks by a Powell off-lattice optimization. In certain cases, this
       resulted in several closely related peaks being explored.  The
       Powell optimization then produced identical structures for these
       peaks. The new peak search algorithm, on the other hand, uses a
       filter to preprocess the peaks found by the exhaustive search.
       This filter already excludes very similar peaks before the Powell
       optimization is run. The net result is a bigger diversity in
       explored peaks with less chance of duplicates being passed to the
       off-lattice optimization portion of the program.

     * The available methods for Euler angle generation in/ colores/ have
       been updated and expanded to include a new "proportional" method.
       This method is now the default and produces more uniform angle
       distributions (very even spacing) than the previously available
       methods.  Euler angles can be inspected using the new /eul2pdb/ tool.

     * For pure cross-correlation calculations and simple refinement of
       manually docked structures, the new /colacor/ tool is now
       available. It is based on the proven framework of /colores/, but
       /colacor/ provides a simple interface solely designed for
       refinement of "approximately docked" structures.

     * The fitting of maps to maps with /colores/ and /colacor/ is now
       supported through the new /pdb2vol/ and /vol2pdb/ conversion tools.

     * Better integration with the free graphics program VMD. VMD now
       directly supports rendering of Situs formatted maps and editing of
       skeletons for motion capture (flexible fitting). The tutorials
       have been updated to reflect these changes. You need VMD 1.8.4a22
       or later
 
<http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD>!

     * Other updates include tools to manipulate maps and PDB files. The
       /voledit/ tool allows the interactive editing and segmentation of
       maps in the Unix shell. The /pdbsymm/ tool generates
       symmetry-related oligomers from monomers, and has been expanded to
       also support C and D symmetries in addition to helices.

     * In addition to electron microscopy, Situs 2.2 provides additional
       support for inclusion of small-angle X-ray scattering data. A new,
       detailed tutorial is available specifically for working with SAXS
       data, and a new tool, /pdb2sax/, was developed for the generation
       of simulated hexagonal bead models for validation of SAXS modeling
       approaches.

     * A fair number of bug fixes is also included in this release. For a
       full list of changes, please visit the history page
       <http://situs.biomachina.org/fhis.html>.









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    David Foster    National Center for Microscopy and Imaging Research
     IT Manager, Programmer   University of California, San Diego
     dfoster[at]ucsd[dot]edu  Department of CRBS, Mail 0608
     (858) 534-7968           http://ncmir.ucsd.edu/
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