scripting_documentation/RosettaScripts/xsd/to_AddCDRProfilesOperation

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) @brief Add Cluster-based CDR Profiles as the task operation for the set of CDRs by default. See ResidueProbTaskOperation for more.

CDR definitions used are North/Dunbrack as the clusters are defined using it.

@details If Cluster-based profiles cannot be used, will use the fallback strategy. This can happen if the the CDR is of an unknown cluster or there is too little data about the cluster to use profiles.

FALLBACK STRATEGIES: seq_design_conservative adds a conservative mutation set to the possible residue types (blosum62 default), seq_design_basic will do nothing (as the default for design is to allow all residue positions); seq_design_none will disable design for that CDR (essentially your saying that if it doesn't have profiles, don't design it)

This TaskOperation is not currently recommended for H3 as it does not cluster well.

Optionally sample whole CDR sequences via the primary strategy of: seq_design_profile_sets (use sets instead of profile probability) seq_design_profile_sets_combined (use profile sets and profile probability)

<AddCDRProfilesOperation name="(&string;)" cdrs="(&string;)"
        fallback_strategy="(seq_design_conservative &string;)"
        include_native_restype="(true &bool;)"
        picking_rounds="(1 &non_negative_integer;)"
        force_north_paper_db="(false &bool;)" use_outliers="(false &bool;)"
        stats_cutoff="(10 &non_negative_integer;)"
        sample_zero_probs_at="(0.0 &real;)"
        cons_design_data_source="(blosum62 &string;)"
        no_probabilities="(false &bool;)" input_ab_scheme="(&string;)"
        cdr_definition="(&string;)" />

cdrs: Which CDRs
fallback_strategy: Strategy to use when there is not enough data to use profiles for a particular CDR cluster
include_native_restype: Should we include the native AA at the position, or not?
picking_rounds: How many times should we choose an AA from the probabilities?
force_north_paper_db: Should we only use the North Paper database, or use newer data if present?
use_outliers: Should we use data for probabilities that includes outliers?
stats_cutoff: If the number of data points for a particular cluster is below this value, we use the fallback strategy instead of cluster sequence profiles
sample_zero_probs_at: If a particular AA has 0 as a probility, whould we keep it at zero or sample it at some probability? Used to increase variability of designs
cons_design_data_source: For conservative design, which blosum matrix should we use?
no_probabilities: Should we sample ALL AA that does not have prob of 0 at 1.0 instead? This basically works to add ALL AA seen at a given position in a particular cluster to the set of design residues. Used to increase variability of designs or for testing purposes
input_ab_scheme: Input Antibody Numbering Scheme. If not set, uses the cmd-line default.
cdr_definition: Input CDR Definition - only works with North currently

scripting_documentation/RosettaScripts/xsd/to_AddCDRProfilesOperation_type