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 August 2026 US-SOMO v4.2.0 (build 9462+)
A note on version numbers: beginning with this update, US-SOMO is identified by the UltraScan release it ships in — v4.2.0 — rather than by a source revision number. A build number is still reported by the program — 9462 or later for this release — and quoting it remains the most useful thing to include when reporting a problem.
The SOMO development line has been merged back into the main UltraScan III line, so everything below is now part of the standard UltraScan/US-SOMO distribution rather than a separate SOMO build.
Summary of New Features in SOMO Software
GRPY Hydrodynamics: Substantially Faster, and Far Less Memory
The GRPY calculation has been rewritten as a new, self-contained C++ solver distributed with US-SOMO. These gains apply to every GRPY run, independently of the shell-reduction option described below:
- Roughly three times less memory. The solver now stores only the upper triangle of the grand mobility matrix, held in tiles and factored in place, and solves directly for the eleven right-hand sides rather than forming a full inverse. Peak memory for an N-bead model falls from about 200N2 to about 60N2 doubles — which roughly doubles the largest structure that will fit in a given amount of memory.
- Multi-threaded throughout. Both the mobility-matrix assembly and the blocked Cholesky factorization are parallelized across all available cores, so the calculation scales with the core count of the machine. Threaded results are identical to the serial ones.
- Single-precision option. Running the factorization in single precision halves the memory again and roughly halves the run time, with all SOMO-reported quantities retained to four significant figures. Precision is selectable from the Hydrodynamics Options panel.
- Pre-flight memory guard. A model too large for the available memory is detected before the calculation begins, with a recommendation to use the ZENO method instead, rather than the machine being driven into swap. This applies to every GRPY run.
- Docker is no longer required. The previous parallel GRPY needed a Docker installation and an external container image. That path has been removed entirely: the solver ships with US-SOMO and needs no separate installation step.
GRPY Shell Reduction for Large Models
- On top of the gains above, GRPY can now compute the hydrodynamic parameters of a structure using only a reduced set of its solvent-exposed beads, working through a series of progressively deeper shells and extrapolating to the full-model result. The saving grows with model size, and is largest exactly where GRPY was previously prohibitive.
- The reduction is self-validating: each run reports an error estimate for the quantity that converged worst, alongside the computed and extrapolated values, so the approximation can be judged rather than assumed. The theory, and guidance on reading the shell report, are documented in the Hydrodynamics Options manual pages.
- The shell-reduction series is capped by the available memory, so it cannot plan a step that will not fit.
- The interface stays live through assembly, factorization and solution; progress is reported throughout; Stop ends a series cleanly and keeps the steps already completed. Optionally, the bead model of each shell step can be written and displayed as it is produced.
- Result files and the saved CSV now carry the GRPY settings that produced them.
Automatic Perception of Non-Coded Residues
Structures containing residues, ligands or cofactors absent from the SOMO tables no longer have to be coded by hand before they can be modeled. US-SOMO can now derive the required properties directly from the coordinates:
- Atomic hybridization, van der Waals radii and electron counts are perceived from the bond graph, including ring perception.
- Partial specific volume is computed with a Durchschlag & Zipper group-contribution engine, in addition using the published metal and ion volumes.
- Anhydrous volume is computed with the standard voxel solvent-excluded-volume approach, implemented natively so that no external tool is required.
- Hydration, based on the values already present in the US-SOMO somo.residue file for specific atoms, is proposed from pH 7 chemistry rules rather than from residue-type averages.
- A review dialog lets the proposed entries be inspected, accepted, edited or skipped before they are used, and a headless perceive command is available for scripted and batch work.
Small-Angle Scattering
- Standard deviation reassessment ("SD rescale"). A new button in the HPLC/KIN S.D. Util mode reassesses the reported experimental errors of an I(q) curve, reporting the applied scale factor and its associated p-value.
- Crop Common no longer drops points where curves differ only in the six-significant-figure rounding of q.
HPLC/KIN and UV-Vis
- The UV-Vis module reads additional data formats and is now scriptable through gui_script commands.
- Smoothing controls are labelled "smoothing radius" throughout, to match what the parameter actually is.
- A crash in the HPLC-SAXS peak end-range clamp has been fixed, along with several dialog and plotting defects.
Molecular Parameter Table Corrections
- Deoxynucleotide C2' hybridization corrected (C4H1 → C4H2).
- SAXS excluded volumes corrected for thirty-five entries in somo.atom.
- NDP ionized-state partial specific volume corrected (0.599 → 0.589).
- Molybdenum cluster support added, completing the Mo series.
- alpha-D-glucose added to somo.residue.
General Improvements
- A modernized RasMol molecular viewer is now included, rebuilt on current graphics libraries and statically linked for distribution.
- Open RasMol molecular viewer windows are now accounted for on exit, and viewers opened by a gui_script are closed with it rather than left orphaned.
- A "Skip deuterium atoms" PDB parsing option has been added, and heavy water is skipped when a structure is loaded.
- The manual has been updated for the changes above, including a new theory page for GRPY shell reduction; pertinent figures will be added later.
Update 17 August 2025 US-SOMO build 7872
Summary of New Features in SOMO Software
Summary of Improvements to the ZENO Method
The ZENO method in the US-SOMO software suite has undergone enhancements to improve its accuracy and reliability in modeling the hydrodynamic properties of large biomolecular structures:
- see Brookes, E., Żuk, P.J. and Rocco, M., 2025. Bead model hydrodynamics: an in-depth comparison between GRPY and ZENO. European Biophysics Journal, pp.1-13. doi: 10.1007/s00249-025-01758-8 for details.
- The sigmodal fit correction of build 7253 has been removed
Update 14 July 2024 US-SOMO build 7253
Summary of New Features in SOMO Software
Hydration and Hydrodynamic Properties
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SOMO now includes a parallel version of the advanced method to calculate the hydrodynamics of bead models with beads of different sizes with overlaps using the Generalized Rotne-Prager-Yamakawa (GRPY) formalism. This method allows for atomic-level representation of proteins, nucleic acids, and carbohydrates.
- Note: To run this GRPY parallel version, you must have Docker installed (for Windows systems, Docker must support Linux containers).
- The improved "van der Waals" (vdW) modeling method calculates pH-dependent bound water molecules for specific atomic groups and adds their volume to the corresponding bead volume.
- This approach uses an Accessible Surface Area (ASA) screening to hydrate only exposed atomic groups, ensuring accurate modeling of hydrodynamic properties.
- Evaluations with 26 well-characterized proteins show highly accurate predictions for the translational diffusion coefficient (Dt), intrinsic viscosity ([η]), and rotational correlation time (τh).
- The method is efficient, allowing routine computations on standard multi-core PCs for structures up to ~100 kDa and supports larger structures with the ZENO method.
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:
- Adjustable "Skin" Parameter:
- The ZENO method now includes an adjustable "skin" parameter, which can be fine-tuned based on a sigmoidal correlation with the gyration radius.
- Improved Accuracy:
- The updated ZENO method shows only minor deviations from the GRPY results, ensuring that it provides a reliable alternative for hydrodynamic calculations, especially for larger structures that are computationally intensive for the GRPY method.
Multi-Angle Light Scattering (MALS) Integration
- SOMO's Small-Angle Scattering (SAS) module now includes Multi-Angle Light Scattering (MALS) data processing and analysis.
- MALS data can be analyzed independently or combined with SAXS data collected using in-line size-exclusion chromatography (SEC) or in batch/kinetic mode.
- Significant improvements have been made to the Gaussian decomposition of SEC-SAXS data, which will be shortly available also for MALS data.
- Integrated MALS+SAXS data analysis extends the scattering vector q range and allows for the recovery of important time-resolved parameters such as molecular weight and radii of gyration.
- A new UV-VIS module allows the analysis of time-resolved multi-wavelength data, including a full scattering correction.
These updates significantly enhance SOMO's ability to model and analyze biomolecular structures, offering improved accuracy and new functionalities for researchers.
General Improvements
- Enhancements have been made to the plotting in the SOMO SAXS HPLC/KIN (formerly HPLC-SAXS) module along with stability and performance 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:
- P(r) functions now support curves with standard deviations.
- Calculation of Rg from P(r) is performed automatically with all plots & loads of P(r) curves.
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Both I(q) and P(r) fits have the following new options:
- Use standard deviations in fits (if present)
- Save NNLS fit information to a CSV file
- Plot NNLS contributing curves
- An important bug-fix to the calculated vbar of structures with non coded residues (Automatic Bead Builder). Thanks to Ute Curth for discovering this issue.
- In batch mode, when all models of a multi-model PDB are selected, the PDB is split into single model temporary files, allowing much larger multi-model PDB files to be processed due to the lower memory requirements.
- US-SOMO managed temporary directories are checked and cleared (subject to clicking "OK") if they exceed a set size (default 50MB, configurable).
US-SOMO Web now available!
Features of US-SOMO Web not present in the desktop version include:
- Support for mmCIF file input
- Ability to directly compute properties of AlphaFold models by providing a UniProt accession code
- SESCA circular dichroism calculations
- Only SoMo Overlap Bead Models and the ZENO method are used with non-modifiable options
- Only the first model of a multi-model structure is processed
- Default configuration files are used and are not editable
- No advanced SAS, HPLC-SAXS nor Batch methods are supported
More details available doi: 10.1007/s00249-023-01636-1
Update 2 April 2021 US-SOMO revision 6005+
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
Update 3 Oct 2018 US-SOMO revision 3165
Update 22 Jan 2018 US-SOMO revision 3141
Intermediate Update 12 December 2017 US-SOMO revision 3112
Update 17 July 2017 US-SOMO revision 3087
Update 20 July 2016 US-SOMO revision 3087
Update 24 March 2016 US-SOMO revision 3047
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.
After installation:
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Get the latest somo.residue.new UPDATED 5 December 2013 - Phosphate group changes and
somo.atom.new files.
cluster.config files.
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.
| System | Typical location |
| OSX US3 | /Applications/ultrascan3/etc |
| Linux US2 | /usr/local/ultrascan/etc |
| Linux US3 | /usr/local/ultrascan3/etc |
| 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 detail:
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!
Mattia
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.
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. |
Mattia Rocco, Ph.D. |