[RASMB] New UltraScan versions available

[Borries Demeler]

Dear UltraScan Users:

Please read below about an important update to the UltraScan-SOMO suite,
as announced by Emre Brookes and Mattia Rocco.

Regards, -Borries


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Dear UltraScan-SOMO users and newcomers:


Following the succesful workshops at the San Antonio AUC 2012 conference
in March, we have prepared an "intermediae" release of the US-SOMO
software. While a full new US-SOMO release is still in the making,
we'd like to announce an "intermediate" release of US-SOMO for Linux,
Windows and Mac systems. Besides several bug fixes, this version has
many new features, additions and improvements, among which are:

1-A revised somo.residue file in which the partial specific volumes
of inorganic ions have been re-calculated from the molar volumes
values present in Table III of Durchschlag and Zipper, Prog. Colloid
Polym. Sci. 94:20-39,1994. Previously, and erroneously, these psv values
were computed directly from the ions' radii. For some cations, like Ca++
and Mg++, the psv assumes relatively large negative values (which also
required changes in the main program coding to handle them). We apologize
for this mistake. While the effect on proteins is likely small, it is
probably more relevant for peptides and nucleic acids.

2-A revised Cluster access module. Access to some of the XSEDE
(formerly TeraGrid) resources and the Alamo cluster at the UTHSCSA is
now available. There are further improvements planned to this facility,
but it is basically functional to compute SAXS curves on large numbers of
structures and to perform discrete molecular dynamic simulations. Cluster
usage can now be granted to users upon request. Hopefully, this will
enable more users to take advantage of these resources.

3-A functional PDB editor, which has some nice features like being able
to split up a multi model PDB file and join individual files.  You can
also check your structure for errors with respect to the US-SOMO residue
table and search for alternate matching residues.  It is still under
development, but is useable.

4-In the SAXS/SANS module, there are now multiple methods for computing
the scattering curve, including a full Debye (requiring explicitly
hydrated structures), and interface with CRYSOL (which should be
downloaded separately).  There is also the ability to compute the distance
distribution function p(r) vs. r from structures and a method to display
a colored contribution of atoms to regions of the p(r) in the molecular
viewer. Best fit and least squares methods of curves to experimental
data are also included.

5-A model classifier, functional to rank batches of results from
hydrodynamic computations against experimental values in various ways.

6-We also offer another hydrodynamic computation method, Zeno, based
on the analogy between electrostatics and hydrodynamics (see the Zeno
website, http://www.stevens.edu/zeno/). We have not yet completed a
comparison of this method vs. our standard Garcia de la Torre-Bloomfield
method, but we plan to do this shortly.  A newer version will be available
in the next release featuring faster processing times.

And importantly, our new home is: http://somo.uthscsa.edu

These updates are available in the latest release of the UltraScan-II
and UltraScan-III versions. You can download the software from the 
usual place, http://www.ultrascan.uthscsa.edu (just follow the 
download link for either UltraScan-II or UltraScan-III).