SampleRotamersFromPDB

Limit rotamer sampling to rotamers that are similar (+/- 5 deg. difference) to rotamers from either input PDBs or a rotamer database file (see RotLibOut). The PDB files are given through the "-packing::unboundrot" flag. For each residue in the input pose a vector of rotamers is constructed from all residues that are structurally aligned between the pose residue and all the input PDBs. Note that the taskoperation does not align the input PDBs and the pose, it only determines which residues are structurally aligned. The alignment should be done before using this TaskOperation.

<SampleRotamersFromPDB name="(&string;)" add_rotamer="(1 &bool;)"
        debug="(0 &bool;)" ccd="(1 &bool;)" aligned_positions="(&int_cslist;)" >
    <Segments name="(&string;)" >
        <Segment name="(&string;)" pdb_profile_match="(&string;)" rot_lib="(&string;)" />
    </Segments>
</SampleRotamersFromPDB>

add_rotamer: If true, add the sampled rotamer to rotamer vector, otherwise just delete rotamers that are not in input pdbs/rotamer database
debug: make output more verbose
ccd: do not modify residues with CUT_LOWER/CUT_UPPER property
aligned_positions: only apply to this taskoperation to specific positions.

Subtag Segments: Wrapper for multiple segments tags

Subtag Segment: individual segment tag

pdb_profile_match: text file matching pdb name to profile
rot_lib: string mapping profile to rotamer database file

Examples

Example 1 - Using input pdbs to modify pose rotamers

<SampleRotamersFromPDB name="example1" add_rotamer="1" debug="0" ccd="0"/>

Example 2 - Using Rotamer database files to modify the pose's rotamer vector

<SampleRotamersFromPDB name="example2" add_rotamer="1" debug="0" ccd="1">
  <Segments>
    <Segment name="frm1" pdb_profile_match="pdb_profile_match" rot_lib="2vc5B:2vc5B_frm1.dat,1hzyB:1hzyB_frm1.dat"/>
    <Segment name="frm2" pdb_profile_match="pdb_profile_match" rot_lib="2vc5B:2vc5B_frm2.dat,1hzyB:1hzyB_frm2.dat"/>
    <Segment name="frm3" pdb_profile_match="pdb_profile_match" rot_lib="2vc5B:2vc5B_frm3.dat,1hzyB:1hzyB_frm3.dat"/>
  </Segments>		
</SampleRotamersFromPDB>

SampleRotamersFromPDB