In this module, you can set some options affecting both the model building and the hydrodynamic computations stages. The Calculate vbar checkbox allows the computation of the partial specific volume (vbar) in standard
conditions (water @ 20°C) of the structure from its composition, using the residues' values stored in the residue table (default: active).
The Covolume [cm^3/mol]: field controls the addition of a covolume term (see Durchschlag and Zipper, Progr. Colloid. Polym. Sci. 94:20-39, 1994) to the calculation of the molar volume of an entire PDB structure, independently of how many chains it is composed from. Since this term was first added in the calculation of relatively small molecules (e.g., amino acids), and, as stated in the Durchschlag and Zipper paper quoted above "In the case of polymers the contribution of Vcv has to be neglected if the volume of the monomeric unit is to be calculated", we chose to add it just once per protein structure, although this is a matter of debate. (default: 12.4 cm3/mol)
Alternatively, a vbar value (vbar(ent), either computed by other means or measured) can be entered in the Enter a vbar value (cm^3/g) field. For instance, if a significant number of non-coded or incomplete residues are skipped when parsing the PDB file, the computed vbar could be not correct; likewise, if the Automatic Bead Builder is used for non-coded residues, the vbar could also be incorrect. In these cases, entering an experimental value will be the best option. Importantly, the temperature T(ent) at which the entered vbar(ent) has been measured/computed must be entered in the Vbar measured/computed at T=°C: field. The vbar(ent) and T(ent) values will be then used by the Hydrodynamic Computation Options module to calculate an operational vbar valid for the temperature conditions to which the hydrodynamic computations are referred. If a vbar value is entered in this field (and the Calculate vbar checkbox is deselected), a message will be displayed in the progress window ("ATTENTION: vbar = ") when the model is being built. This should avoid the use of incorrect external vbar values resulting by inadvertently leaving the Calculate vbar checkbox deselected from a previous model-generating session.
The Select vbar button will instead load a vbar value calculated from protein sequence by using the UltraScan vbar calculation routine. WARNING: whenever possible, use experimental vbar values, as many factors can affect its computation!!!! The routines provided here should be considered just as a best approximation in absence of experimental data.
The Hydration Water Vol. (A^3) field sets the volume of the water of hydration molecules, which has been found (Gerstein and Chothia, Proc. Natl. Acad. Sci. USA 93:10167-10172, 1996) to be on average 24.5 Å3, different from that of either bulk (29.7 Å3) or isolated (11.5 Å3) water molecules (default: 24.041 Å3).
The Enable Peptide Bond Rule checkbox controls if the peptide bond rule is used by the SoMo method. With this rule, the peptide bond segment is used for the main chain beads of a protein structure. These beads are thus positioned at the cog of the (CA-C-O)n-(N)(n+1) atoms, except when PRO is the (n+1) residue. In this case, the peptide bond bead is positioned at the cog of the (CA-C-O)n atoms. Additional rules control the generation of the OXT bead and of the first N atom at the beginning of each protein chain. All these rules are controlled by "special" residues in the somo.residue table. To gain total control over the positioning, volumes and masses of every bead, the Enable Peptide Bond Rule checkbox should be deselected. In this case, the descriptions present in the somo.residue table are fully effective. (default: selected).
The Average Parameters for Automatic Bead Builder: submenu contains a series of fields governing the average parameters that will be used by the Automatic Bead Builder routine when this option is selected (see
here) for non-coded residues.
The Bead model controls are user-defined parameters that were introduced in April 2012 and still need further testing, used when loading a bead model for SAXS computations.
In May 2014 we added a new method for the computation of the hydrodynamic parameters starting from an atomic-level structure, the boundary elements approach BEST [S.R. Aragon, A precise boundary element method for macromolecular transport properties. J. Comp.Chem., 25, 1191-1205 (2004); S.R. Aragon and D.K. Hahn, Precise boundary element computation of proteins transport properties: Diffusion tensors, specific volume and hydration, Biophysical Journal, 91:1591-1603 (2006)]. This method necessitates a properly formatted atomic radii and names file for its ancillary program MSROLL, and the one provided with the original BEST program is directly made available within the US-SOMO implementation ("best.radii"). Users wishing to utilize instead the atomic radii and names as listed in the US-SOMO somo.residue file can generate a properly formatted file compatible with BEST by selecting the Create MSROLL atomic radii and names file on load residue file checkbox here, and re-launch US-SOMO.
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Last modified on September 8, 2020.