Welcome to US-SOMO

US-SOMO icon

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 17 July 2017 US-SOMO revision 3087

If you are attending the workshop at AUC 2017, please install the software beforehand.

Update 20 July 2016 US-SOMO revision 3087

A new version of US-SOMO with HPLC tools and sample data is available here. This includes updates as described in

Brookes et al. (2016) "US-SOMO HPLC-SAXS Module: Dealing with Capillary Fouling, and Extraction of Pure Component Patterns from Poorly Resolved SEC-SAXS Data", J. Appl. Cryst. 49.

Update 24 March 2016 US-SOMO revision 3047

In preparation for the upcoming SSRL SAXS workshop, we have prepared an updated version of US-SOMO with improved HPLC-SAXS tools. A summary page for student attending the workshop is here.

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)

Dear UltraScan-SOMO users and newcomers:

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.

After installation:

Important Update 3 March 2013

Dear UltraScan-SOMO users and newcomers:

Peter Zipper has recently discovered some errors in the distributed version of the somo.residue file of US-SOMO. I paste below his comments:

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

Dear UltraScan-SOMO users and newcomers:

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:

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: