RepeatPropagationMover

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RepeatPropagationMover

Propagates a protein X times

Autogenerated Tag Syntax Documentation:

XRW TO DO

<RepeatPropagationMover name="(&string;)"
        first_template_res="(9999 &non_negative_integer;)"
        last_template_res="(9999 &non_negative_integer;)"
        numb_repeats="(&non_negative_integer;)" ideal_repeat="(true &bool;)"
        repeat_without_replacing_pose="(false &bool;)"
        maintain_cap="(false &bool;)"
        maintain_cap_sequence_only="(false &bool;)"
        nTerm_cap_size="(&non_negative_integer;)"
        cTerm_cap_size="(&non_negative_integer;)"
        maintain_ligand="(false &bool;)"
        extract_repeat_info_from_pose="(false &bool;)"
        extract_repeat_template_repeat="(1 &non_negative_integer;)"
        start_pose_numb_repeats="(4 &non_negative_integer;)"
        start_pose_length="(0 &non_negative_integer;)"
        start_pose_duplicate_residues="(0 &non_negative_integer;)" />

first_template_res: first template residue
last_template_res: last template residue
numb_repeats: (REQUIRED) number of repeats to output
ideal_repeat: is the repeat internally ideal
repeat_without_replacing_pose: for speed when the duplicating the same length pose
maintain_cap: if you want the cap structure and sequence maintained
maintain_cap_sequence_only: maintain only the sequence in cap
nTerm_cap_size: Size of n_term of cap
cTerm_cap_size: Size of c_term of cap
maintain_ligand: maintain ligand
extract_repeat_info_from_pose: mode where repeat info is extracted from input pose
extract_repeat_template_repeat: location where repeat info is extracted from input pose
start_pose_numb_repeats: number of repeats in input pose
start_pose_length: orig length of input pose. This is used to catch pose length changes
start_pose_duplicate_residues: used when only 1 repeat in input pose and there are identical residues in N_term and C_term

General options

numb_repeats : numb of repeats in output pose
ideal_repeat="false" #copies bond lengths in addition to phi/psi/omega

Use case 1: extract all necessary info from the repeat itself

numb_repeats=length
extract_repeat_info_from_pose="true"
start_pose_numb_repeats="3"

Use case 2: You know where the pose starts/stops and has some cap sequence

first_template_res="51"
last_template_res="100"
maintain_cap_sequence_only="true"
numb_repeats="6"
nTerm_cap_size="50" #will maintain the sequence of these 50 residues
cTerm_cap_size="50" #will maintain the sequence of these 50 residues

Use case 3: One repeat in the original pose + some extra non repeating stuff

name
numb_repeats
extract_repeat_info_from_pose="true"
start_pose_numb_repeats="1"
ideal_repeat="false" #copies bond lengths in addition to phi/psi/omega
start_pose_duplicate_residues="19" #number of extra residue