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 14 July 2024 US-SOMO revision 7253+

Summary of New Features in SOMO Software

Hydration and Hydrodynamic Properties

Summary of Improvements to the ZENO Method

The ZENO method in the US-SOMO software suite has undergone significant enhancements to improve its accuracy and reliability in modeling the hydrodynamic properties of large biomolecular structures:

Multi-Angle Light Scattering (MALS) Integration

These updates significantly enhance SOMO's ability to model and analyze biomolecular structures, offering improved accuracy and new functionalities for researchers.

General Improvements

Update 14 March 2023 US-SOMO revision 6730+

An update to US-SOMO has been released. The focus of this release is on SOMO SAS updates, which include:

Other new features include:

US-SOMO Web now available!

US-SOMO Web, https://somoweb.genapp.rocks, provides a convenient way to compute hydrodynamic, structural and circular dichroism calculations.
Features of US-SOMO Web not present in the desktop version include: Limitations of the web version: We will gladly consider feature enhancement of US-SOMO Web, please contact us via the Feedback tab on US-SOMO Web or email us directly.
More details available doi: 10.1007/s00249-023-01636-1

Update 2 April 2021 US-SOMO revision 6005+

A major update to US-SOMO has been released. This update focuses on improvements to hydrodynamic calculations.

The Generalized Rotne-Prager-Yamakawa (GRPY) method (Zuk et al. Biophys. J. 115:782-800, 2018) has been integrated. This method allows the computation of all the hydrodynamic parameters (translational diffusion and sedimentation coefficients, relaxation time, intrinsic viscosity) with high accuracy for models that can have overlapping beads of different sizes. It is, however, computationally intensive, limiting its application when large structures are studied, for which the ZENO method is a viable option if calculation of rotational diffusion is not required. A parallel version of GRPY will be included in a future release.

Additional features:

Upon loading a PDB structure, a search for disulfide-bonded and free cysteines is performed, enabling discrimination between the molecular properties of cystine versus cysteine when beads are generated and parameters such as the partial specific volume are computed. While this information can be already present in the PDB “SSBOND” field(s), this is not always the case.
The temperature and the pH at which the experimental data were collected can now be entered. The latter, coupled with information of the pK of ionizable residues now present in the somo.residue file, controls the ionization state of atoms, resulting in a more sound evaluation of the molecular weight, and of hydration, the latter an important parameter in the generation of appropriate bead models. Changes were made in the somo.residue editor to deal with this new feature.

Numerous other enhancements and bug-fixes have been included. Some of these enhancements are described in the 2021 Edition of Encyclopedia of Biophysics Chapter entitled "US-SOMO: Methods for Construction and Hydration of Macromolecular Hydrodynamic Models". The changes are also described and documented in the various help pages included with US-SOMO and available online.

Click link in sidebar for "install" instructions.

Update 5 November 2018 US-SOMO revision 3167

An updated US-SOMO has been released. These include improvements to the layout for smaller screen sizes, a simplified installation for Windows, and a few bugfixes. Click link in sidebar for "install" instructions.

Update 3 Oct 2018 US-SOMO revision 3165

An improved US-SOMO with updates to the HPLC-SAXS routines has been released. A tutorial will be held as part of the BioSAS: Advanced Applications course at SAS2018. Notes and special instructions for this tutorial are here. Click link in sidebar for "install" instructions.

Update 22 Jan 2018 US-SOMO revision 3141

An updated US-SOMO with an improved ZENO implemention, including support for multi-core processors on all operating systems has been released. This update includes improvements to the hydrodynamic section of US‑SOMO, adding a direct atom-to-beads utility (vdW), and to the small-angle scattering modules, such as the inclusion of an indirect Fourier transform method with a Bayesian approach for the computation of the distance distribution function P(r) vs. r in real space from scattering intensity as a function of momentum transfer I(q) vs. q in reciprocal space. Click link in sidebar for "install" instructions.

Intermediate Update 12 December 2017 US-SOMO revision 3112

US-SOMO has been integrated into UltraScan III versions 3.5 & 4.0. You can obtain these new versions here. This includes the newer faster and threaded version of 2ENO for all 64 bit platforms.

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:

If you would like a live tutorial over Skype or Google hangouts, please send an email.

If you have any questions, please feel free to contact us directly.

Emre Brookes, Ph.D.
Associate Professor for Research
Department of Chemistry & Biochemistry
The University of Montana, Missoula

Mattia Rocco, Ph.D.
Retired, Proteomica e Spettrometria di Massa
IRCCS Ospedale Policlinico, San Martino

Genova, Italy