scripting_documentation/RosettaScripts/xsd/mover_AlignPDBInfoToSequences

Autogenerated Tag Syntax Documentation:

Align the PDBInfo of a pose to some given sequences. This mover does not alter geometry or sequence of the pose. The only thing that is altered is the PDBInfo. The goal of this mover is to re-number/re-chain a pose so that its PDBInfo is in sync with some reference. There are two modes. In 'single' mode all the target sequences are appended in order and the entire pose is aligned to that sequence. In 'multiple' mode we attempt to align the sequence of each chain of the pose to each of the target sequences. If we experience a perfect match, we will renumber based on that target sequence. For more information, please reference the online documentation. WARNING 1: if you have a very long sequence, (1000s of residues) this protocol can use a lot of memory due to the SmithWaterman alignment. Be cautious of this. WARNING 2: This will most likely not give you the correct results if your pose or target sequence contain carbohydrate or other residues that are represented using [ ] or ( ).

<AlignPDBInfoToSequences name="(&string;)" mode="(&string;)"
        json_fns="(&string;)" throw_on_fail="(false &bool;)"
        sequence_alignment_cut_max="(10 &positive_integer;)" >
    <Target name="(&string;)" sequence="(&string;)" chains="(&string;)"
            segmentIDs="(&string;)" insCodes="(&string;)"
            residue_numbers="(&string;)" />
</AlignPDBInfoToSequences>

mode: (REQUIRED) Which mode to run in. options: ['single', 'multiple']
json_fns: The name of the json sequence file(s) (separated by ',')
throw_on_fail: throw on failure.
sequence_alignment_cut_max: Maximum number of cuts to allow when doing the sequence alignment.

Subtag Target: Targets and settings of the sequences to align to.

sequence: (REQUIRED) sequence of current chain/protein
chains: (REQUIRED) chains to set with current protein
segmentIDs: segmentIDs to set for the current protein
insCodes: insertion codes to set for the current protein
residue_numbers: Residue numbers to set for current chain (must be of size 1 (used as a starting number), or the size of 'sequence', or empty)

scripting_documentation/RosettaScripts/xsd/mover_AlignPDBInfoToSequences_type