Welcome to US-SOMO
Welcome to the US-SOMO website.
UltraScan Solution Modeler (US-SOMO) processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity, and small angle scattering curves, that contribute to our understanding of molecular structure in solution. Knowledge of biological macromolecules' structure aids researchers in understanding their function as a path to disease prevention and therapeutics for conditions such as cancer, thrombosis, Alzheimer's disease and others. US-SOMO provides a convergence of experimental, computational, and modeling techniques, in which detailed molecular structure and properties are determined from data obtained in a range of experimental techniques that, by themselves, give incomplete information.
Update 22 May 2014 US-SOMO revision 2717
In preparation for the upcoming ACA conference, we have prepared an updated version of US-SOMO with improved HPLC-SAXS tools. The release US3 version for Linux and OSX can be downloaded here. If you are a windows or Ubuntu linux user, we recommend the better performing (esp. with the HPLC-SAXS tools) US2 windows version here with install details here or Ubuntu & RedHat binary versions here HPLC-SAXS experimental data files for the workshop are available as a zip file or gzipped tarball.
Announcement US-SOMO Intermediate Release 27 April 2014
In conjunction with the release of UltraScan III 3.0, we have provided an intermediate release of US-SOMO which can be downloaded here.
Included in this update are multiple improvements to the UltraScan III version of US-SOMO.
Highlights include: addition of an interface for BEST [S.R. Aragon. J. Comput. Chem. 25:1191-1205] hydrodynamic computations which compliment the existing SOMO / AtoB and ZENO methods already implemented and inclusion of the HPLC-SAXS tools E Brookes et al. J. Appl. Cryst. 46, 1823-1833].
There have also been multiple minor improvements to the interface for the UltraScan III version, including a helpful directory history system which remembers visited directories across sessions.
Note that the UltraScan II version of US-SOMO was previously advanced from the UltraScan III version. These are now in sync and will remain so until the eventual deprecation of the UltraScan II version.
Please give it a try and let us know if you run into any problems.
Important Update 11 November 2013
(further updated 11 April 2014)
(updated to version 2504: 23 November 2013)
The latest version of US-SOMO including the new HPLC SAXS tools is available here. We will be preparing a geneal release before the ACA meeting where we have a dedicated session on HPLC-SAXS (4.2.4) and a special tutorial session on the US-SOMO HPLC-SAXS tools (2.2.6).
The current US-SOMO release version is 1927
To get started, you can look at the SOMO Manual
US-SOMO is bundled as part of the UltraScan software. For all Linux, Windows, and Macintosh (running OSX 10.5 or older version), we recommend downloading the US-II version here. For Macintosh users running OSX 10.6 or newer, we recommend downloading the US-III version here.
Get the latest somo.residue.new UPDATED 5 December 2013 - Phosphate group changes and
These files contains updated residues and will always be the latest versions.
They should be placed in the system ultrascan/etc directory.
Note: these may require administrator permissions to install on your system.
|Windows (EN) US2||\Program Files\ultrascan\etc|
|Windows (EN) US3||\Program Files\ultrascan3\etc|
After correctly placing the file, the next startup of US-SOMO will request the installation of the files and will back up the current ones. Again, this may require administrator privileges.
Important Update 3 March 2013
Peter Zipper has recently discovered some errors in the distributed version of the somo.residue file of US-SOMO. I paste below his comments:
In my recent tests using Ultrascan 9.9 Rev. 1831 I encountered a discrepancy between the molecular weights of RNA chains as reported by Ultrascan and the results obtained from my programs. When I analyzed the discrepancy in more detail I could localize its origin very soon. I detected that in the Ultrascan file somo.residue the nucleobases are not represented with the correct number of hydrogen atoms but are lacking between 1 and 3 hydrogens.
in adenine one hydrogen is missing at C2;
in cytosine one hydrogen is missing at C5 and one at C6;
in guanine one hydrogen is missing at N1 and two are missing at N2;
in uracil one hydrogen is missing at N3, C5, and C6, respectively;
in thymine one hydrogen is missing at N3 and one at C6.
I do not understand why these hydrogens are not taken into account in your somo.residue file. But perhaps you can give me a simple explanation.
As a matter of fact, Peter was absolutely correct, and I take full responsibility for that, it was sloppy entering on my part. I apologize for any inconvenience this might have caused, and I am grateful to Peter for having uncovered these mistakes. I have now corrected them, and new versions of the somo.residue and somo.atom files are made available for downloading (see the "After installation:" notes at the top of this webpage for instructions). Beside the corrections, the new somo.residue now contains hydroxyproline, more alternate names for nucleotides (wish there was a strict convention on PDB atoms naming to which all software adhered...), Triton X-100 (with different chain lengths), Mn and Mg ions, AMP, ATP, ATF, and explicit water of hydration (for SAXS simulations, the structures must hydrated using external programs). If you have coded for new atoms/residues using US-SOMO, you should pick those bits from your current tables and add them to the new tables, an operation that can be done using any text editor (however, should anyone feel uneasy to do so, you can send me your somo.atom and somo.residue files, and I will insert the extra residues/atoms in either the current distribution, or, if you want to keep it private, I will email the corrected files back to you).
Best wishes to you all, and happy hydrodynamic/SAS modeling with US-SOMO!
Intermediate Release Announcement
While a full new US-SOMO release is still in the making, we'd like to announce an "intermediate" release of US-SOMO for Linux, Windows and Mac systems. Besides several bug fixes, this version has many new features, additions and improvements, among which are:
- A revised somo.residue file in which the partial specific volumes of inorganic ions have been re-calculated from the molar volumes values present in Table III of Durchschlag and Zipper, Prog. Colloid Polym. Sci. 94:20-39,1994. Previously, and erroneously, these psv values were computed directly from the ions' radii. For some cations, like Ca++ and Mg++, the psv assumes relatively large negative values (which also required changes in the main program coding to handle them). We apologize for this mistake. While the effect on proteins is likely small, it is probably more relevant for peptides and nucleic acids.
- A revised Cluster access module. Access to some of the XSEDE (formerly TeraGrid) resources and the Alamo cluster at the UTHSCSA is now available. There are further improvements planned to this facility, but it is basically functional to compute SAXS curves on large numbers of structures and to perform discrete molecular dynamic simulations. Cluster usage can now be granted to users upon request. Hopefully, this will enable more users to take advantage of these resources.
- A functional PDB editor, which has some nice features like being able to split up a multi model PDB file and join individual files. You can also check your structure for errors with respect to the US-SOMO residue table and search for alternate matching residues. It is still under development, but is useable.
- In the SAXS/SANS module, there are now multiple methods for computing the scattering curve, including a full Debye (requiring explicitly hydrated structures), and interface with CRYSOL (which should be downloaded separately). There is also the ability to compute the distance distribution function p(r) vs. r from structures and a method to display a colored contribution of atoms to regions of the p(r) in the molecular viewer. Best fit and least squares methods of curves to experimental data are also included.
- A model classifier, functional to rank batches of results from hydrodynamic computations against experimental values is various ways.
- We also offer another hydrodynamic computation method, Zeno, based on the analogy between electrostatics and hydrodynamics (see the Zeno website, http://www.stevens.edu/zeno/). We have not yet completed a comparison of this method vs. our standard Garcia de la Torre-Bloomfield method, but we plan to do this shortly. A newer version will be available in the next release featuring faster processing times.
We will be starting our mailing list with the next release. If you wish to be added to the mailing list or would like a live tutorial over Skype or EVO, please send an email.
Please use the following citations for your publications:
For the use of the US-SOMO program:
- Rai, N, Nollmann, M, Spotorno, B, Tassara, G, Byron, O, and Rocco, M. SOMO (SOlution MOdeler): Differences between X-Ray and NMR-Derived Bead Models Suggest a Role for Side Chain Flexibility in Protein Hydrodynamics. Structure 13, 723-734, 2005,
- Brookes, E., Demeler., B, and Rocco, M. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. Eur. Biophys. J, 2010 DOI: 10.1007/s00249-009-0418-0
- Brookes, E., Demeler, B., Rosano, C., and Rocco, M. Developments in the US-SOMO Bead Modeling Suite: New Features in the Direct Residue-to-Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening, , Macromol. Biosci. 10:746-753, 2010 DOI: 10.1002/mabi.200900474
- For A to B usage:
- For HPLC-SAXS and SVD usage
For Parsimonious models usage
- Brookes, E. Parsimonious modeling, (manuscript in preparation)
- For CRYSOL usage
- For DAMMIF usage
- For DAMMIN usage
For DMD usage:
- Dokholyan, NV,Buldyrev, SV, Stanley, HE, and EI Shaknovich. Discrete molecular dynamics studies of the folding of a protein-like model . (1998) Folding & Design 3:577-587
- Ding F, Dokholyan NV. Emergence of protein fold families through rational design. Public Library of ScienceComput Biol. (2006) 2(7):e85
- For GASBOR usage
For ZENO usage:
- Mansfield et al., Intrinsic Viscosity and the Electric Polarizability of Arbitrarily Shaped Objects, Phys. Rev. E, 64:61401-61416, 2001
For BEST usage:
- S.R. Aragon, A precise boundary element method for macromolecular transport properties J. Comp.Chem., 25, 1191-1205 (2004).
And also please cite for specific utilities used within US-SOMO:
If you have any questions, please feel free to contact us directly.
We look forward to hearing from you!
Emre Brookes, Ph.D.
Mattia Rocco, Ph.D.