[RASMB] ANNOUNCE: New UltraScan release

[Borries Demeler]

Dear Colleagues,

I am happy to announce UltraScan II release 857. 

This UltraScan release contains a series of minor bug fixes and enhancements,
and one major update to the SOMO module. This is the beta-2 release of SOMO,
and we hope the final beta release. This represents several months of hard
work by Emre Brookes and Mattia Rocco, and the results you obtain now with 
SOMO are of production quality. New releases for Mac OSX 10.4 and 10.5, Linux
32- and 64-bit, and Windows XP and Vista are provided on the UltraScan website:

http://www.ultrascan.uthscsa.edu/

Source code can be obtained from the UltraScan tracking Wiki:

http://wiki.bcf.uthscsa.edu/ultrascan/

To get your copy, please click on the "Download" button and select "UltraScan Software". 

Below is a list of the new features in SOMO:

UltraScan includes an embedded BETA2-version of the bead modeling suite
SOMO (Brookes et al., Eur. Biophys. J., in press, 2009).

This release is the final beta-release. Please send all bugs, comments
and suggestions for improvements to the UltraScan development team on
the UltraScan Wiki pages: http://wiki.bcf.uthscsa.edu/ultrascan/ The
main characteristics, operation, and testing of this beta-1 version are
described in a paper in press (Brookes et al., Eur. Biophys. J., 2009).

Summary of Changes between beta-1 and beta-2:

   1. The Grid module is now more reliable, although some features are
   still unavailable. In particular, we have separated Grid operations
   that can be made on PDB structures from those that can be taken on
   previously-generated bead models. In the GUI main panel, these two
   modes are now accessed from separate buttons, and only the former
   is available when a PBD file is loaded. The latter becomes available
   once a bead model has been generated, or a previously-generated bead
   model file is loaded. In addition, the ASA re-check control for the
   Grid module has now its own settings, avoiding confusion with the
   SOMO method settings.

   2. Still in the main GUI panel, we have added an Automatically
   Calculate Hydrodynamics checkbox, that will allow to proceed to the
   computational phase as soon as a bead model is generated, without
   halting operations. This is particularly useful when large or multiple
   models are being built, allowing unattended operation. However,
   we recommend to still visually check the generated bead models,
   an operation that can also be done after the completion of the
   hydrodynamic computations.

   3. The full range of options for dealing with non-coded
   residues, and/or missing atoms within coded residues, has now been
   implemented. Although it must be underscored that these are approximate
   methods, and that complete structures and fully coded residues will
   give the most reliable results, these features allow the on-the-fly
   processing of virtually any kind of PDB-formatted file.

   4. The defaults for all the parameters and options are now stored
   in a file. Upon starting, US-SOMO checks every parameter against
   the defaults, and warns the user if some are different. Likewise,
   every time a parameter is changed from the option menus, a warning
   is printed in the progress window.

   5. If manual settings are chosen for the vbar and/or the total mass
   of the model, these values are printed in the progress window under
   an "Attention" label. This should avoid using wrong values left-over
   from a previous session.

   6. The parameters used in bead model generation are printed in the
   progress window when loading a previously-generated US-SOMO model.

   7. The iterations progress for the ASA and supermatrix inversion
   routines are now printed in a black-background window below the
   main progress window, allowing a more in-depth check of the status
   of operations. For small to medium size models, this will be barely
   noticeable, but it should become more evident when processing larger
   structures.

   8. The synchronous overlap removal routines have been now fully tested,
   and appear to be working fine. While the hydrodynamic parameters
   of models of small test proteins produced in this way are nearly
   indistinguishable from those produced by the default hierarchical
   procedure, the models do look "better", with a more uniform aspect
   and less gaps between beads. The major drawback is the appreciably
   longer times required to remove the overlaps with this procedure, so
   for the moment being the hierarchical procedure is still the default.

   9. Note that we fixed two errors with the vbar computation which
   could effect hydrodynamic results produced by our beta-1 release. One
   caused the automatically computed vbar value to be off by .002. The
   other occurred when multiple models hydrodynamics were simultaneously
   processed: each received the same vbar.

   10. SOMO is now bundled with RASMOL binaries on all platforms, and 
   RASMOL is used as an integrated viewer for SOMO.

Please note that some changes in the GUI interface have been made in
respect to that described in the paper. The beta-2 release comes with
a comprehensive and up-to-date manual, whose pages can be accessed from
the Help buttons in the various US-SOMO modules.

We believe that this beta-2 version of US-SOMO can now be safely used
to determine the hydrodynamic properties of biomacromolecules starting
from their 3D atomic structures.

Happy Hydrodynamics to everyone!