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 14 July 2024 US-SOMO revision 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. |