Rmsd

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Rmsd

Autogenerated Tag Syntax Documentation:

Filter based on the C-alpha RMSD to a reference structure.

<Rmsd name="(&string;)" reference_name="(&string;)" symmetry="(0 &bool;)"
        chains="(&string;)" superimpose_on_all="(false &bool;)"
        superimpose="(1 &bool;)" threshold="(5 &real;)" by_aln="(&bool;)"
        aln_files="(&string;)" template_names="(&string;)"
        query_names="(&string;)" rms_residues_from_pose_cache="(1 &string;)"
        confidence="(1.0 &real;)" >
    <rmsd resnum="(&refpose_enabled_residue_number;)"
            pdb_num="(&refpose_enabled_residue_number;)" />
    <span begin_res_num="(&refpose_enabled_residue_number;)"
            begin_pdb_num="(&refpose_enabled_residue_number;)"
            end_res_num="(&refpose_enabled_residue_number;)"
            end_pdb_num="(&refpose_enabled_residue_number;)" />
    <span_two begin_native="(&non_negative_integer;)"
            end_native="(&non_negative_integer;)"
            begin_pose="(&non_negative_integer;)"
            end_pose="(&non_negative_integer;)" />
</Rmsd>

reference_name: Name of reference pose to use (Use the SavePoseMover to create a reference pose)
symmetry: Should we be symmetry-aware?
chains: Chain characters without separation
superimpose_on_all: Do we want to superimpose on all residues?
superimpose: Do we want to superimpose?
threshold: Threshold in RMSD above which the filter fails
by_aln: Perform RMSD calculation as guided by a sequence alignment file
aln_files: Comma-separated list of alignment files
template_names: Comma-separated list of template names
query_names: Comma-separated list of query names
rms_residues_from_pose_cache: Are the RMS residues stored in the Pose's cache?
confidence: Probability that the pose will be filtered out if it does not pass this Filter

Subtag rmsd:

resnum: Residue number for the beginning of the alignment region
pdb_num: Residue number for the beginning of the alignment region

Subtag span:

begin_res_num: Residue number for the beginning of the alignment region
begin_pdb_num: Residue number for the beginning of the alignment region
end_res_num: Residue number for the end of the alignment region
end_pdb_num: Residue number for the end of the alignment region

Subtag span_two:

begin_native: Residue number for the beginning of the alignment region, on the native
end_native: Residue number for the end of the alignment region, on the native
begin_pose: Residue number for the beginning of the alignment region, on the pose
end_pose: Residue number for the end of the alignment region, on the pose

Calculates the Calpha RMSD over a user-specified set of residues. Superimposition is optional. Selections are additive, so choosing a chain, and individual residue, and span will result in RMSD calculation over all residues selected. If no residues are selected, the filter uses all residues in the pose.

By default, the RMSD will be calculated to the input pose (pose at parse time). Use -in:file:native <filename> or reference_name= to choose an alternate reference pose.

chains: list of chains (eg - "AC") to use for RMSD calculation
pdb_num/res_num: see RosettaScripts#rosettascripts-conventions_specifying-residues
residue: add a new leaf for each residue to include (can use rosetta index or pdb number)
span: contiguous span of residues to include (rosetta index or pdb number)
threshold: accept at this rmsd or lower
superimpose: perform superimposition before rmsd calculation?
reference_name: If given, use the pose saved with the SavePoseMover under the given reference_name as the reference.
by_aln: align pose to the relative pose according to a sequence alignment.
aln_files: fasta format alignment files with the query and the template
template_names: name of the relative pose, as is written in the aln_files
query_names: name of the query pose, as is written in the aln_files

Rmsd

Rmsd

See also