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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;" id="docs-internal-guid-828f291d-7fff-941d-b4b9-cafac71de999"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Dear RASMB members,</span></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">A major update US-SOMO has been released. This update focuses on improvements to hydrodynamic calculations.</span></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">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.</span></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Additional features:</span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">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.</span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">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.</span></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">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" available at </span><a href="https://link.springer.com/referenceworkentry/10.1007/978-3-642-35943-9_292-1" style="text-decoration:none;"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">https://link.springer.com/referenceworkentry/10.1007/978-3-642-35943-9_292-1</span></a><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">. The changes are also described and documented in the various Help pages included with US-SOMO and available online.</span></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Get the latest information and download instructions at </span><a href="https://somo.aucsolutions.com" style="text-decoration:none;"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">https://somo.aucsolutions.com</span></a></p>
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<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Best regards,</span></p>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;"><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Emre Brookes </span><a href="mailto:emre.brookes@umontana.edu" style="text-decoration:none;"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">emre.brookes@umontana.edu</span></a></p>
<span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">Mattia Rocco </span><a href="mailto:mattia.rocco@quipo.it" style="text-decoration:none;"><span style="font-size:11pt;font-family:Arial;color:#1155cc;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:underline;-webkit-text-decoration-skip:none;text-decoration-skip-ink:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;">mattia.rocco@quipo.it</span></a><span style="font-size:11pt;font-family:Arial;color:#000000;background-color:transparent;font-weight:400;font-style:normal;font-variant:normal;text-decoration:none;vertical-align:baseline;white-space:pre;white-space:pre-wrap;"> (please note new email !)
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