[RASMB] UltraScan v. 9.9 released

[Borries Demeler]

Dear Colleagues,

I am happy to announce the release of UltraScan v9.9.

This release offers a few new features, and many bugfixes and upgrades.

New features include a fitter for nonlinear velocity models using
genetic algorithm optimization on the supercomputer. This methods 
allows fitting of any general model of non-interacting and reacting
systems with an arbitrary number of reactions. The reactions can be 
kinetically limited and k_off rates and equilibrium constants can now
be derived from the velocity experiments. For more information, please
get a copy of our paper:

Cao, W and B. Demeler. Modeling Analytical Ultracentrifugation Experiments
with an Adaptive Space-Time Finite Element Solution for Multi-Component
Reacting Systems. Biophys. J. (2008) 95(1):54-65
(http://www.demeler.uthscsa.edu/ultrascan-publications/CaoDemeler-biophysj-2008.pdf)

On the maintenance side, UltraScan now has a completely reworked
archiving/compression system built in based on GNU tar/gzip. This is
used in the up/download of data to/from the USLIMS database and for
archiving of data. The code now includes tar and gzip routines natively
built into UltraScan and works identically on all platforms. This avoids
the problems with large files previously encountered under Windows. The
entire upload and download process has been worked over and is now much
more user friendly and robust.

Most notably, we have now integrated the SOMO SOlutionMOdeler from 
the Rocco/Byron labs in UltraScan, thanks to the help from Mattia Rocco.
For those of you attending the UltraScan workshop at the Newcastle conference,
we will demonstrate the program there. While the program is fully functional,
we can right now not guarantee that all hydrodynamic values derived from
PDB files are reliable until we have done further testing. So, your mileage
may vary. Please read Mattia's announcement of this UltraScan component
below.

UltraScan is a GPL licensed software which you can freely download, including
source.

Precompiled binaries for native versions in Linux (32 and 64 bit), Mac
(intel and G3/4) and Windows (intel 32 and 64 bit), as well as an ISO
CDROM image of a Linux distro, and a Linux VMWare Image that can be run
under Windows are all available from:

http://www.ultrascan.uthscsa.edu

Source code can be downloaded using svn from the UltraScan tracking wiki:

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

Please let us know if you find any issues or problems with this release.
Those of you with Slackware UltraScan Linux distributions please leave your
computer on for 24 hours and it will update itself.

Thank you, -Borries Demeler

Here is the UltraScan-SOMO announcement from Mattia Rocco:

> "Within this UltraScan release, you will find an alpha version of a new, 
> improved implementation of the SOMO (SOlution MOdeller) bead modelling 
> suite for the computation of the hydrodynamic properties starting from 
> atomic structures (Rai et al., Structure 13:723-734, 2005). The main 
> principles behind SOMO is to convert into beads groups of atoms within 
> protein residues, include in the bead volumes the theoretically bound water 
> of hydration, correctly  place the beads in space, and remove the overlaps 
> between the beads. The approach taken in SOMO thus differs fundamentally 
> from either shell- or grid-based methods. However, the original SOMO was a 
> collection of programs mostly working only under the Linux operating 
> system, and requiring extensive interaction with a series of sequential 
> commands to operate.
> 
> In the redesign of SOMO for incorporation in the UltraScan suite, we have 
> paid particular attention to:
> 1 - Every operation is now done through the UltraScan Graphic User 
> Interface (GUI), with clearly labeled buttons. SOMO has a main, simple 
> window from which various options-setting pop-up windows can be called.
> 2 - Maximum flexibility in the kind of residues that can be modeled as 
> beads. The old SOMO was limited to the standard amino acids, a few 
> carbohydrates moieties, and just a single detergent (octyl glucoside), thus 
> excluding, for instance, the possibility of modeling nucleic-acid-protein 
> complexes. An extensive set of table-building utilities now allow EVERY 
> kind of atom present in the PDB files to be recognized and modeled. A set 
> of basic tables is distributed with this release, and the user can edit 
> them at will. Future releases will include expanded tables, based also on 
> the feedback from users.
> 3 - A PDB file parser that recognizes the relevant fields, and warns if 
> non-coded residues are present or if some residues have missing atoms. The 
> parser is able to distinguish multiple models coming from NMR experiments 
> and allows the choice of the model to be analyzed. In future developments, 
> we plan to allow multiple models to be analyzed sequentially and their 
> parameters averaged.
> 4 - A new Accessible Surface Area (ASA) algorithm, based on SurfRacer 
> (Tsodikov et al., J. Comput. Chem. 23:600-609, 2002) for the identification 
> of buried residues, allowing the exclusion of buried beads from the 
> hydrodynamic computations, thus reducing the computational load and 
> extending the size range of structures that can be modeled.
> 5 - Direct visualization of both the original structure and of the bead 
> model using RasMol.
> 6 - An extensive, on-line Manual explaining the meaning of all the features 
> and options, with the default settings highlighted.
> 
> While we encourage UltraScan users to test and familiarize themselves with 
> the new SOMO version, we warn that this alpha version has NOT been yet 
> fully tested for the reliability of its end products, the hydrodynamic 
> parameters computed for the bead models. We plan to reach a beta version 
> stage were results can be fully trusted well before the end of the year. In 
> the meantime, feedback from "testers" will be VERY much appreciated, both 
> in terms of signalling of bugs and suggestions on how to make 
> easier/clearer/generally improved the program"
> 
---
Borries Demeler, Ph.D.
Associate Professor
The University of Texas Health Science Center at San Antonio
Dept. of Biochemistry, MC 7760
7703 Floyd Curl Drive, San Antonio, Texas 78229-3901
Voice: 210-567-6592, Fax: 210-567-1136, Email: demeler at biochem.uthscsa.edu