[RASMB] New UltraScan II release

[Mattia Rocco]

Dear Colleagues,

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.

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
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:

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 you'll find a list of the new features in SOMO.
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 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).

Summary of Changes from beta-2 and this full release:

1. The main GUI has been completely reworked, with a three-panels 
subdivision reflecting the various different steps:

         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)

         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).

         Hydrodynamic Calculations - giving access to the computation of 
the hydrodynamic parameters and viewing the results.

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
produced by the hierarchical procedure for SoMo-kind models. See below for
its use in the Grid-based approach.

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:

         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
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
of course already edit the somo.residue table to this end, if they wish.

         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
(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.

         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
the default option).

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
give the most reliable results, these features allow the on-the-fly 
processing of virtually any kind of PDB-formatted file.

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:

         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
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).

A FULLY FUNCTIONAL SAXS CURVE GENERATOR IS NOT YET AVAILABLE, SO THE 
"Compute SAXS Curve" BUTTON IS NOT ACCESSIBLE IN THIS RELEASE.

         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.

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.

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.

As usual, Happy Hydrodynamics to everyone!

Mattia Rocco & Borries Demeler


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