Oct. 14th, 2009:
UltraScan 9.9 rev. 973 released -- Please check the SVN Trac log for details on bug fixes in the revision history.
Announcement of release 973:
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:
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.
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).
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.
As usual, Happy Hydrodynamics to everyone!
Mattia Rocco & Borries Demeler
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Last modified on Jan. 25, 2009.