Applying NCS to a molecule to generate all NCS copies with apply_ncs



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.


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


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:


Additional information

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