PoseFromSequenceMover

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PoseFromSequenceMover

Autogenerated Tag Syntax Documentation:

This is a mover that can create a pose from a sequence, or fasta. if you use a fasta that has multiple sequences in it, and use the 'use_all_in_fasta' tag (set to true) it will use all of the sequences in the fasta and separate them by '/'. Also you can build the pose extended if you set the 'extended' tag.

<PoseFromSequenceMover name="(&string;)" fasta="(&string;)"
        sequence="(&string;)" use_all_in_fasta="(false &bool;)"
        extended="(false &bool;)" residue_type_set="(fa_standard &string;)" />

fasta: Fasta file name
sequence: sequence as a string
use_all_in_fasta: instead of using only first sequence in a fasta, use them all (and join them via '/')
extended: extend the pose
residue_type_set: Residue representation, centroid, fa_standard

The goal of this mover is to allow you to build a pose of your chosen sequence without requiring -s or -in:file:fasta

If this is the first stage in your rosetta script, you should supply In general, you should add the commandline flag -input_empty_pose true so that rosetta starts with the pose made by this mover, instead of creating one from the pdb or fasta supplied.

One of the nice things about this mover is that you can create multi-chain Poses easily by supplying a fasta file that has multiple sequences ie:

>Thiswillbechain1
SEGVENCE
>Thiswillbechain2
POTBELLG

will yield a pose with two chains: SEGVENCE and POTBELLG

This is particularly useful with long complicated Poses supplied to the Hybridize mover, where it is useful to know the identities of the chains of the pose when generating inputs.