Author(s)

• apply_ncs: Tom Terwilliger

Purpose

If you have a single copy of your molecule placed in the crystal and you have a set of NCS operators defined in an ncs_info.ncs_spec file (such as that written by phenix.find_ncs), you can apply the operators to your molecule to generate all the NCS copies. This can be useful if you want to work on one molecule in your asymmetric unit and propagate it to the other copies. You can generate your ncs_info.ncs_spec file using phenix.find_ncs and your original model containing all the NCS copies, then apply it to any one of the individual molecules to regenerate the others.

Usage

How apply_ncs works:

apply_ncs assumes that you are supplying it with one copy of your molecule, placed in your unit cell, and that you are also supplying a ncs_info.ncs_spec file that contains all the NCS operators for your structure along with the approximate molecular centers where each operator applies. apply_ncs assumes that the NCS operator with a center closest to the center of the molecule you supply (including space-group symmetry) is the operator corresponding to your input molecule.

apply_ncs then calculates the transformation for your molecule to molecule 1, and then uses all the NCS operators to transform molecule 1 to each NCS copy.

Output files from apply_ncs

apply_ncs.pdb: A PDB file with your input molecule placed at all the NCS-related positions in your structure

Examples

Standard run of apply_ncs:

Running apply_ncs is easy. From the command-line you can type:

phenix.apply_ncs  mol1.pdb my_ncs.ncs_spec

If apply_ncs chooses the wrong NCS copy to match up to your input molecule, you can tell it which one your input molecule is with match_copy:

phenix.apply_ncs mol1.pdb my_ncs.ncs_spec match_copy=2

apply_ncs will then assume that you are inputting ncs copy 2.

Possible Problems

Specific limitations and problems:

Literature

Additional information

The documentation for find_ncs describes how to find and apply NCS information for helical arrays, point-group symmetry, and non-point-group symmetry.

List of all available keywords

• apply_ncs
  • job_title = None Job title in PHENIX GUI, not used on command line
  • input_files
    • pdb_in = None Input PDB file
    • ncs_in = None File with NCS operators to be applied to pdb_in This can be a .ncs_spec file from find_ncs, simple_ncs_from_pdb or find_ncs_from_density It can also be NCS formatted for resolve, including rotations, translations, and centers NOTE: NCS operators only apply to a limited region within the unit cell. The center of this region for molecule 1 (the one you enter with pdb_in) is specified by the NCS center for molecule 1. If your molecule in pdb_in is not near this, then it will be brought as close as possible using space-group symmetry (as defined in the CRYST1 record of pdb_in) before application of NCS. If your molecule is closer to the center for operator k, then it will instead be brought to that center and then transformed to all other locations
    • map_in = None CCP4 or MRC-style map file (required if trim_overlapping=True). Map must cover the entire molecule including NCS copies.
  • output_files
    • target_output_format = *None pdb mmcif Desired output format (if possible). Choices are None ( try to use input format), pdb, mmcif. If output model does not fit in pdb format, mmcif will be used. Default is pdb.
    • pdb_out = apply_ncs.pdb Output PDB file
    • log = apply_ncs.log Output log file
    • params_out = apply_ncs_params.eff Parameters file to rerun apply_ncs
    • write_refine_ncs_out = False Write out refine_ncs_out file for refinement
    • refine_ncs_out = apply_ncs_refine.eff NCS formatted for refinement. This will put all of the input chains as reference and all of the ncs-related chains in selection records, one for each NCS copy applied.
  • directories
    • temp_dir = "temp_dir" Optional temporary work directory
    • output_dir = "" Output directory where files are to be written
    • gui_output_dir = None
  • ncs
    • trim_overlapping = False Trim pieces that overlap (including those overlapping by NCS). Requires a full-size (not boxed) map file (ccp4/mrc). Also requires resolution of the map.
    • resolution = None Map resolution (for trim_overlapping)
    • match_copy = None Force input model to be associated with NCS copy match_copy This can be useful if your molecule center is close to an NCS center other than the one it is associated with
    • no_match_copy = None Do not allow input model to be associated with this NCS copy no_match_copy. This can be useful if your molecule center is close to an NCS center other than the one it is associated with
    • apply_operators_directly = False You can apply the NCS matrices directly to an input model, without considering one of the NCS copies to be the identity for this model.
    • max_copies = None You can limit the number of NCS copies to fewer than the actual number
    • start_copy = None You can start the NCS copies with any available copy
    • only_start_copy = None Just use start_copy and do not try to arrange chain names
    • unique_only = None Just use unique part of pdb_in
    • chain_names = None You can specify the chain names to generate. Note: there must be exactly the same number of chain_names as total chains generated by apply_ncs. This includes any chains that are just waters or ligands.
    • used_chain_id_list = None You can specify chain names not to generate
    • use_space_group_symmetry = True Normally apply_ncs uses space-group symmetry read from your input PDB file to find the appropriate operator. To disable this say use_space_group_symmetry=False. This is what you should do if you are using space group P1 as a dummy space group for example.
  • control
    • verbose = False Verbose output
    • raise_sorry = False Raise sorry if problems
    • debug = False Debugging output
    • dry_run = False Just read in and check parameter names
    • resolve_command_list = None You can supply any resolve command here NOTE: for command-line usage you need to enclose the whole set of commands in double quotes (") and each individual command in single quotes (') like this: resolve_command_list="'no_build' 'b_overall 23' "