[3DEM] new release of 'Situs' hybrid modeling package
David Foster
foster at ncmir.ucsd.edu
Wed Oct 19 13:28:04 PDT 2005
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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>.
--
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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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