length by which Cas are allowed to go for the duration of backbone minimization before a penalty is assigned.
This is typically performed in calculation of SASA, and in reality is among the defining characteristics of SASA. Switch this off to estimate the Area Place rather.
Ramachandran map which is the common of all canonical L amino acids, flattened to give equal chance on the permitted region, Using the permitted area picked with superior stringency, and symmetrized. Lazily loaded; for sampling only.
Names on the residue-style-set patches which ought to be utilized whether or not excluded/commented out in patches.txt; useful for screening non-default patches
skips all style steps. WARNING: will only output centroid stage structures and dump all fragment attempts.
Specify what to do when community queue is full: block and wait for packets to get be send out or drop payload
if possibility -detect_design_interface is Energetic, invoking this selection causes all residues that happen to be within just the required cuts of any catalytic residue site can also be set to developing/repacking
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Do an ensemble look for where by Every single input pdb is used for an ensemble centered lookup. Instead of Every in file outputting nstruct, we utilize the input data files to make a complete nstruct through the inputs
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The amount of atom overlap authorized concerning upstream and downstream atoms inside of a match. If This is often unspecified around the command line, then the value click here to find out more during the bump_tolerance alternative is utilised
make starting composition from a file that contains H/C/E to explain topology or B/P sample, has fasta file format
Specify the file exactly where glycosidic linkage conformer torsion angle statistical facts is saved. The default directory is databases/chemical/carbohydrates/linkage_conformers/but any route can be furnished. The default filename is default.desk
Through Stage two docking and refinement, the frequency at which a full packing operation by using the PackRotamersMover needs to be applied.