[RASMB] New UltraScan release

[Borries Demeler]

Dear Colleagues,

I am happy to announce a new release of UltraScan 9.9 (release ver. 1100).
The new release contains a number of bug fixes and feature enhancements,
most notably in the US-SOMO module, which are further described below.

UltraScan is free and open source, and source code and binaries for Linux,
Macintosh and Microsoft windows (XP, Vista, Windows 7) can be obtained
from our website: http://www.ultrascan.uthscsa.edu
(please note installation comment for Windows 7 on the download page).

Best regards, -Borries

P.S. We will teach a workshop on UltraScan and SOMO bead modeling on
June 4-8 in San Antonio. Registration information at:

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

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This new US-SOMO release contains a number of major improvements
and bug-fixes. Within the rigid-body hydrodynamics framework, this
can be considered a fully functional release producing reliable,
publication-quality parameters, especially for what concerns translational
diffusion properties. Using the direct correspondence method (SoMo)
method, an accuracy within ±2% should be expected for the calculation
of the translational diffusion coefficient of rigid biomacromolecules
for which all residues/atoms are present and are properly defined in the
somo.residue table. As for the sedimentation coefficient, its accuracy
depends also on the partial specific volume; our tests indicate that
an experimental value is advisable, as it produces more consistent
results, usually within ±3%, while the accuracy decreases to within
±5% using computed psv values. The rotational diffusion and intrinsic
viscosity accuracies are more difficult to evaluate, given the greater
uncertainties in the experimental data, but can be expected between
±5-10%. Further work is in progress to improve these computations,
which are heavily dependent on the volume correction used.

New features and improvements:

1-The AtoB (Grid) method is now also fully functional, and performs as well 
as the direct correspondence method, especially at high grid resolution 
(3-5 A). The improvements have been made possible by the assignment of the 
theoretically-bound water of hydration at the atom level instead than at 
the residue level (see point 2), and by the installment of a screening 
procedure distinguishing exposed from buried beads before overlap 
reduction, allowing the outward translation of the exposed beads.

2-The somo.residue editor allows the definition the water of hydration at 
the atom level within each residue, which can, however, be bypassed to 
assign a global residue value. In the somo.residue table distributed with 
this version, the atomic hydration has been already defined for the amino 
acid residues only, while global residue hydration values are defined for 
all other residues. We will post updated somo.residue tables when they will 
become available. Users are also encouraged to send us any somo.residue 
tables containing new residue or changes in residues properties that they 
might have developed.

3-US-SOMO can now fully process PBD files with missing atoms within coded 
residues or with non-coded residues, using the PDB parsing options 
provided. This should allow for a quick, although potentially less 
accurate, evaluation of the hydrodynamic parameters of such files. BE AWARE 
THAT FOR ACCURATE HYDRODYNAMIC COMPUTATIONS, ALL ATOMS PRESENT IN SOLUTION 
SHOULD BE REPRESENTED IN THE ATOMIC STRUCTURE!

4-The thermodynamic conditions (solvent temperature, viscosity, and 
density) at which the parameters are computed can now be changed at will in 
the Hydrodynamic Computations Options panel (the default is still water @ 
20 °C). A buffer name and acronym can be entered as well, and printed in 
the output files. The partial specific volume is also corrected for the 
chosen temperature, but the value stored in the bead model files is ALWAYS 
that at 20 °C.

5-The computed parameters can now be optionally saved in a comma-separated 
format in an additional file, for easy importing into spreadsheets. The 
parameters to be saved can be chosen from a dedicated menu.

6-A batch mode processing capability has been implemented, allowing the 
uploading of multiple files and their unattended processing. The files can 
be either PDB or previously-generated bead models. The batch module 
pre-screens the files to verify that they comply with the current settings 
(completeness and coding of residues, overlaps in bead models), prompting 
for corrective action to be taken, if necessary. Batch loading also permits 
the computation of the average parameters of the models, something that 
previously was available only for NMR-style PDB files.

7-The SAXS/SANS module is still under development, but the P(r) vs. r 
computation is already operational. For PDB files, three options are 
offered, Raw (simple computation of the pairwise distance between the 
atoms), SAXS (weighted by the number of electrons in each atom), and SANS 
(weighted by the neutron scattering lengths of the atoms at the set D2O 
fraction). For bead models, only the Raw calculation is currently 
implemented. Absolute and normalized P8r) values are computed, and stored 
in a single file.

Important bug fixes:

1-The water density and viscosity at 20 °C values, Avogadro's  number 
and  Boltzmann's constant used in the previous US-SOMO releases had 
slightly different values from the current accepted values, used elsewhere 
in UltraScan. While this resulted in relatively minor errors in the 
hydrodynamic parameters computations (<1%), this has now been fixed. The 
water density viscosity at 20 °C values can nevertheless be changed at will 
in the Hydrodynamic Calculations options panel, while Avogadro's number and 
Boltzmann's constant can be accessed from the main UltraScan menu.

2-Precision/rounding issues in the MW calculations produced slightly 
different MW values when different bead generation options were used 
(especially using the Grid procedure). This has now been fixed.

Final note: most improvements/additions in the new release are described 
and tested in a paper in press (Brookes et al., Macromol. Biosci.)