In the Miscellaneous parsing options subpanel, the first three options listed are not presently selectable, and are currently hard-coded in the program. The the fourth has just (September 2020) been made operational (default: selected), and the other two are new additions.
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Skip hydrogen atoms. Explicit hydrogen atoms are found in NMR- or neutron crystallography-derived structures, and are not coded for in the distributed somo.residue file. Therefore, the parser automatically skips any line containing them. In the current SOMO implementation, the hydrogen atoms are "included" in the heavy atoms to which they are bound, but we do not exclude to make the skipping as an option to allow users to explicitly treat hydrogens; obviously, this will call for a re-definition of all atoms and residues in the somo.hybrid, somo.atom, and somo.residue files.
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Skip solvent water molecules. In the current US-SOMO implementation, the water of hydration is treated in a statistical manner. Therefore, lines in PDB files coding for explicit crystallographic water molecules are automatically skipped. However, we plan to make this as an option in the future, since one might wish to investigate the effect of the crystallographic waters on the hydrodynamics, or to use artificial hydration schemes employing explicit water molecules. As for the previous field, using explicit waters will also call for a re-definition of the hydration numbers in the somo.residue file.
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Skip alternate conformations. PDB files sometimes contain alternate coordinates for particular atoms within residues. It is presently not possible to explore the effect of these alternate conformations, which should be negligible anyway. Therefore, presently US-SOMO uses only the first ("A") alternate conformation by default. In the future, we might provide the choice between the alternate conformations.
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Find free SH, change residue coding. In the somo.residue file, cysteine (CYS) is treated as if it's always engaged in a S-S bond with another cysteine (a cystine pair). This is because currently there's no distinction in PDB files between cysteines and cystines. Since this involves slightly different physico-chemical parameters (e.g., two H atoms are lost when a S-S bridge is formed), we now offer an automatic "free SH" finder. The loaded PDB structure will be scanned and the mutual spatial distance between every the SG atom in CYS residues (if present) will be measured. Every CYS-CYS pair for which the spatial distance between their SG atoms is below the cut-off value listed in the Disulfide distance threshold [A]: field (default: 2.5 Å) will be identified as disulfide-bonded and listed in the right-side progress window of the main US-SOMO panel. Any CYS residue for which the SG atom isn't within bonding distance from another CYS SG atom will be considered as a free SH, and its residue name will be changed to CYH, for which the coding is already provided within the somo.residue file.
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Save CSV on load PDB. If this checkbox is selected, when you load a pdb a csv file is created with the following columns:"Atom number","Atom name","Residue number","Residue name","Radius","Mass [Da]","X","Y","Z". The Radius and Mass fields are populated using values stored in the somo.residue file (note that the mass includes any ionized weight difference). The file is placed in the user's ultrascan/somo/tmp directory and it is listed in the text area: "Created CSV atomic file: filename-with-path".
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Use explicit WAT radii as specified in the PDB T-factor field. This is an experimental option that allows modeling explicit water molecules (using WAT as a residue name), with a specific radius (Å) defined in the temperature-factor ("T-factor") field in PDB files.
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