Finding NCS from density in a map with find_ncs_from_density



find_ncs_from_density is a tool to identify NCS relationships directly from an electron density map specified with a map coefficients file. It writes out the NCS operators in a format that can be read by find_ncs and by the PHENIX wizards. Usually find_ncs_from_density is used through find_ncs (phenix.find_ncs contains find_ncs_from_density).


How find_ncs_from_density works:

Output files from find_ncs_from_density

find_ncs_from_density.ncs_spec: A formatted file that can be read by phenix.find_ncs and the PHENIX wizards that specifies the NCS operators. temp_dir/ncs_avg_map_coeffs.mtz: This is an mtz file with just one averaged NCS region written out in space group P1.


Standard run of find_ncs_from_density:

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

phenix.find_ncs_from_density  map_coeffs.mtz

Possible Problems

If your molecule is large, you may wish to increase the radius used for NCS identification (density_radius) and the peak separation (peak_separation). If your molecule has pseudo-symmetry you may also want to increase these parameters.

If you know how many NCS copies are present, you may wish to specifying that with ncs_copies_max.

If you want to have the program look much harder for NCS, try the keyword n_center_use=20 (or some other number larger than 1). It will then take the top 20 positions found with guess_molecular_centers and try each one as a center for a molecule (instead of trying just the top 1 position).


Finding non-crystallographic symmetry in density maps of macromolecular structures. T.C. Terwilliger. J Struct Funct Genomics 14, 91-5 (2013).

List of all available keywords