ClashCheck

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ClashCheck

Autogenerated Tag Syntax Documentation:

Calculate the number of heavy atoms clashing between building blocks.

<ClashCheck name="(&string;)" clash_dist="(3.5 &real;)"
        sym_dof_names="(XRW TO DO &string;)"
        nsub_bblock="(1 &non_negative_integer;)"
        cutoff="(0 &non_negative_integer;)" verbose="(0 &bool;)"
        write2pdb="(0 &bool;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" confidence="(1.0 &real;)" />

clash_dist: Distance between heavy atoms below which they are considered to be clashing. Note: A hard-coded cutoff of 2.6 is set for contacts between backbone carbonyl oxygens and nitrogens for bb-bb hbonds.
sym_dof_names: Only use with multicomponent systems. Comma-separated list of name(s) of the sym_dof(s) corresponding to the building block(s) between which to check for clashes.
nsub_bblock: The number of subunits in the symmetric building block. Does not need to be set for multicomponent systems.
cutoff: Maximum number of allowable clashes.
verbose: If set to true, then will output a pymol selection string to the logfile with the clashing positions/atoms.
write2pdb: If set to true, then will output a pymol selection string to the output pdb with the clashing positions/atoms.
task_operations: A comma-separated list of TaskOperations to use.
packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).
confidence: Probability that the pose will be filtered out if it does not pass this Filter

Note: only works in symmetry mode.

ClashCheck

ClashCheck

See also