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<font size=3>Dear Colleagues,<br><br>
we are happy to announce that a new release of UltraScan II, # 973,
containing several improvements to the US-SOMO module, has been made
available.<br><br>
This UltraScan release also contains a new model builder module that
fixes a bug with invalid parameter initializations. Major changes have
been made to the SOMO module, which now is released as our first
production version. This advance has been made possible by several months
of hard work mainly by Emre Brookes, but Bruce Dubbs and Jeremy Mann have
also made <br>
significant contributions to porting the program to various operating
systems. New releases for Mac OSX 10.4 and 10.5, Linux 32- and 64-bit,
and Windows XP and Vista are therefore provided on the UltraScan
website:<br><br>
</font><font size=3 color="#0000FF"><u><a href="http://www.ultrascan.uthscsa.edu/" eudora="autourl">http://www.ultrascan.uthscsa.edu/<br><br>
</a></u></font><font size=3>Source code can be obtained from the
UltraScan tracking Wiki:<br><br>
</font><font size=3 color="#0000FF"><u><a href="http://wiki.bcf.uthscsa.edu/ultrascan/" eudora="autourl">http://wiki.bcf.uthscsa.edu/ultrascan/<br><br>
</a></u></font><font size=3>To get your copy, please click on the
"Download" button and select "UltraScan
Software".<br><br>
Below you'll find a list of the new features in SOMO. <br>
Please send all bugs, comments and suggestions for improvements to the
UltraScan development team on the UltraScan Wiki pages:<br><br>
</font><font size=3 color="#0000FF"><u><a href="http://wiki.bcf.uthscsa.edu/ultrascan/" eudora="autourl">http://wiki.bcf.uthscsa.edu/ultrascan/<br><br>
</a></u></font><font size=3>The main characteristics, operation, and
testing of the earlier US-SOMO beta versions are described in a paper in
press (Brookes et al., Eur. Biophys. J., 2009?, doi
10.1007/s00249-009-0418-0). The new additions will be described in paper
that will be submitted to Macromolecular Bioscences as a part of the 18th
AUC conference proceedings special issue (Brookes et al., to be
submitted).<br><br>
Summary of Changes from beta-2 and this full release:<br><br>
1. The main GUI has been completely reworked, with a three-panels
subdivision reflecting the various different steps:<br><br>
<x-tab> </x-tab>PDB
Functions - which controls the operations regarding choosing the PDB
file, selecting the model(s) if multiple models are present, and
view/editing the file, if necessary. In addition, there's a new button
giving access to a SAXS simulation module (see below)<br><br>
<x-tab> </x-tab>Bead Model
Functions - which includes all the bead modeling operations, like
building SoMo or Grid models, viewing the ASA results, and loading a
previously-generated bead model. A new button giving access to SAXS
calculations on a bead model is also present here (see below).<br><br>
<x-tab> </x-tab>Hydrodynamic
Calculations - giving access to the computation of the hydrodynamic
parameters and viewing the results.<br><br>
2 - The synchronous overlap reduction option has been now further tested,
and can be considered a valid alternative to the hierarchical procedure.
It is more time-consuming, but produces "better looking"
models, whose hydrodynamic properties are, however, nearly
indistinguishable from those <br>
produced by the hierarchical procedure for SoMo-kind models. See below
for <br>
its use in the Grid-based approach.<br><br>
3 - The Grid module has undergone a major reworking, and its performance
can now match or exceed (especially at very low grid sizes, =< 3
Angstroms) that of the SoMo procedure. This has been made possible by two
main new features:<br><br>
<x-tab> </x-tab>The
theoretical hydration can be now directly assigned at the atom level,
instead that at the residue level. The somo.residue file and editor have
been changed accordingly, and proper values for amino-acids have been
already entered in the distributed file (it's, however, still possible to
<br>
override the atomic values and enter a global value for each residue).
With this change, the Grid models of proteins can now be properly
hydrated. We plan to make soon the transition to the atomic level
hydration also for the other kind of residues (like nucleotides and
carbohydrates), but users can <br>
of course already edit the somo.residue table to this end, if they
wish.<br><br>
<x-tab> </x-tab>An ASA
screening has been introduced after primary bead generation. This allows
discriminating between surface-exposed and buried beads. For the former
category, the outward translation procedure is now available when
removing overlaps, and this preserves the original <br>
(hydrated) surface much better. An ASA re-check can also be performed on
the final model, allowing a much better discrimination between buried and
exposed beads in the final, overlap-less bead model.<br><br>
<x-tab> </x-tab>In
addition, the synchronous overlap removal procedure has been also fully
tested in the Grid procedure, and produces much "better
looking" models. Although it can be very time consuming when low
grid sizes are used, it should be preferentially employed here (but has
NOT been made as <br>
the default option).<br><br>
4 - The full range of options for dealing with non-coded residues, and/or
missing atoms within coded residues, has now been fully tested, with
excellent results. Although it must be underscored that these are
approximate methods, and that complete structures and fully coded
residues will <br>
give the most reliable results, these features allow the on-the-fly
processing of virtually any kind of PDB-formatted file.<br><br>
5 - A new SAXS simulation module has been introduced, which, however, is
still a work in progress, with some features already available, and some
not yet ready. Pressing either of the "SAXS Functions" buttons
(see 1- above) will open a pop-up window with two subpanels:<br><br>
<x-tab> </x-tab>In the
first, SAXS Plotting Functions, the generation of a SAXS curve from
either a PDB file or a bead model is controlled, and plotted on a graphic
window. For PDB models, in addition to the somo.atom and somo.hybrid
files, it is necessary to load a third file (automatically done if
present), somo-saxs_atoms, which contains the five-exponential
coefficients of the atomic scattering factors, and the atomic volumes.
This file can be edited from a pull-down menu in the main panel, under
"Lookup Tables" ("Add/Edit SAXS Coefficients"). For
bead models, appropriate scattering <br>
coefficients will be made available in a similar file, also editable (NOT
YET AVAILABLE). The generation of a SAXS curve will be possible by
pressing the "Compute SAXS Curve" button, while another button
allows loading a previously-generated SAXS curve. Importantly, it is also
possible to load a CRYSOL-generated SAXS curve (already
operational).<br><br>
A FULLY FUNCTIONAL SAXS CURVE GENERATOR IS NOT YET AVAILABLE, SO THE
"Compute SAXS Curve" BUTTON IS NOT ACCESSIBLE IN THIS
RELEASE.<br><br>
<x-tab> </x-tab>The second
panel contains a distance distribution function P(r) vs r generator,
which is already functional. The results are plotted in another graphics
window, and previously-generated distributions can be also uploaded. The
bin size in the P(r) vs r can be controlled. The data points are
automatically saved in a file.<br><br>
6 - Changes have been made also to the somo.hybrid and somo.atoms files,
and to their editors, to link them to the SAXS module and the
somo.saxs_atoms file.<br><br>
7 - The HELP menus have been updated to fully describe all these changes,
additions, and improvements, EXCEPT the SAXS module for which the help
section has NOT yet been prepared, since it's still a work in
progress.<br><br>
As usual, Happy Hydrodynamics to everyone!<br><br>
Mattia Rocco & Borries Demeler<br>
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