SeqprofConsensus

Read PSSM sequence profiles and at each position allow only identities that pass a certain threshold in the PSSM. The code mentions symmetry-support, but I haven't tested this.

<SeqprofConsensus name="(&string)" filename="(''&string)" min_aa_probability="(0.0 &Real)" probability_larger_than_current="(1 &bool)" ignore_pose_profile_length_mismatch="(0 &bool)" convert_scores_to_probabilities="(1&bool)"  keep_native="(0&bool)"/>

SeqprofConsensus can also be operated with ProteinInterfaceDesign and RestrictToAlignedSegments task operations contained within it. In that case, three different threshold can be set, one for the protein interface (where residues are marked for design), one for RestrictToAlignedSegments (again, where residues are marked for design), and one for the remainder of the protein. The reasoning is that you may want to be less 'consensus-like' at the active site than away from it. The three cutoffs would then be set by: conservation_cutoff_protein_interface_design, conservation_cutoff_aligned_segments, and min_aa_probability (for the remainder of the protein). The subtags, ProteinInterfaceDesign and RestrictToAlignedSegments are expected to be subtags of SeqprofConsensus and all of the options open to these task operations can be set the same way (the option name is not expected and if you specify it you would generate failure).

filename: of the PSSM. If none is specified, the task operation will attempt to read SequenceProfile constraints directly from the pose, and set up a profile based on those constraints. If those aren't available, expect an exit.
min_aa_probability: the PSSM style log2 transformed probabilities. For instance set to 0 to allow favorable positions, set to 2 to allow very favorable only, and set to -2 to also allow slightly unfavorable identities. The highest-probability identities are always allowed to design, so set to very high values (>10) if you want the highest probability identities to be allowed in design.
probability_larger_than_current: always allow identities with probabilities at least larger than that of the current residue seen in the PDB.
ignore_pose_profile_length_mismatch: if set to 0 this will cause a utility exit if the pose and profile do not match.
convert_scores_to_probabilities: convert the PSSM scores (e.g., -4, +10) to probabilities in the 0-1 range.
keep_native: If set to true adds the native aa identity to allowed identities regardless of min_aa_probability cut-off.

Autogenerated Tag Syntax Documentation:

XRW TO DO

<SeqprofConsensus name="(&string;)" use_occurrence_data="(true &bool;)"
        restrict_to_repacking="(true &bool;)"
        convert_scores_to_probabilities="(true &bool;)" filename="(&string;)"
        min_aa_probability="(&real;)" keep_native="(&bool;)"
        chain_num="(1 &non_negative_integer;)"
        probability_larger_than_current="(&bool;)"
        ignore_pose_profile_length_mismatch="(&bool;)" debug="(false &bool;)"
        conservation_cutoff_aligned_segments="(&real;)"
        conservation_cutoff_protein_interface_design="(&real;)" >
    <ProteinInterfaceDesign name="(&string;)"
            repack_chain1="(1 &non_negative_integer;)"
            repack_chain2="(1 &non_negative_integer;)"
            design_chain1="(0 &non_negative_integer;)"
            design_chain2="(1 &non_negative_integer;)"
            allow_all_aas="(0 &non_negative_integer;)"
            design_all_aas="(0 &non_negative_integer;)"
            jump="(1 &non_negative_integer;)"
            interface_distance_cutoff="(8.0 &real;)"
            modify_before_jump="(true &bool;)" modify_after_jump="(true &bool;)" />
    <RestrictToAlignedSegments name="(&string;)" source_pdb="(&string;)"
            start_res="(&string;)" stop_res="(&string;)"
            chain="(1 &non_negative_integer;)" repack_shell="(6.0 &real;)" >
        <AlignedSegment name="(&string;)" source_pdb="(&string;)" start_res="(&string;)"
                stop_res="(&string;)" />
    </RestrictToAlignedSegments>
</SeqprofConsensus>

use_occurrence_data: Should we restrict positions to mutations that have occurrence larger than zero
restrict_to_repacking: XRW TO DO
convert_scores_to_probabilities: XRW TO DO
filename: XRW TO DO
min_aa_probability: XRW TO DO
keep_native: XRW TO DO
chain_num: XRW TO DO
probability_larger_than_current: XRW TO DO
ignore_pose_profile_length_mismatch: XRW TO DO
debug: XRW TO DO
conservation_cutoff_aligned_segments: XRW TO DO
conservation_cutoff_protein_interface_design: XRW TO DO

Subtag ProteinInterfaceDesign: Restricts to the task that is the basis for protein-interface design.

repack_chain1: first chain to repack
repack_chain2: 2ndchain to repack
design_chain1: first chain to design
design_chain2: 2nd chain to design
allow_all_aas: allow all amino acid types for design. default: do not design to G/C/P
design_all_aas: design all amino acids. default: do not design G/C/P
jump: residue with the jump
interface_distance_cutoff: Cbeta distance of chain where design/repack is allowed on other chain
modify_before_jump: change residues before the jump. For instance, if you want set repack on chain2 interfacial residues to true, and the rest of chain2 to false, and yet not change the task for chain1, then use this taskoperation with modify_before_jump=0
modify_after_jump: change residues after the jump

Subtag RestrictToAlignedSegments: XRW TO DO

source_pdb: XRW TO DO
start_res: XRW TO DO
stop_res: XRW TO DO
chain: XRW TO DO
repack_shell: XRW TO DO

Subtag AlignedSegment: XRW TO DO

source_pdb: XRW TO DO
start_res: XRW TO DO
stop_res: XRW TO DO

SeqprofConsensus

SeqprofConsensus

See Also