|Python-based Hierarchical ENvironment for Integrated Xtallography|
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:
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.
Specific limitations and problems:
List of all find_ncs_from_density keywords
------------------------------------------------------------------------------- Legend: black bold - scope names black - parameter names red - parameter values blue - parameter help blue bold - scope help Parameter values: * means selected parameter (where multiple choices are available) False is No True is Yes None means not provided, not predefined, or left up to the program "%3d" is a Python style formatting descriptor ------------------------------------------------------------------------------- find_ncs_from_density input_files mtz_in= None MTZ file with coefficients for a map labin= "" Labin line for MTZ file with map coefficients. This is optional if find_ncs_from_density can guess the correct coefficients for FP PHI and FOM. Otherwise specify: LABIN FP=myFP PHIB=myPHI FOM=myFOM where myFP is your column label for FP center_pdb_in= None Optional PDB file with list of centers of density to be used as search model density_mtz_in= None MTZ file with coefficients for density around center defined by first atom in center_pdb_in (required) NOTE: Must be in space group p1 with identical cell to mtz_in density_labin= "" Labin line for MTZ file density_mtz_in. This is optional if find_ncs_from_density can guess the correct coefficients for FP PHI and FOM. Otherwise specify: LABIN FP=myFP PHIB=myPHI FOM=myFOM where myFP is your column label for FP output_files centers_pdb_out= guess_molecular_centers.pdb Output PDB file with coords of centers log= find_ncs_from_density.log Output log file ncs_spec_file= 'find_ncs_from_density.ncs_spec' NCS specification file with all NCS information params_out= find_ncs_from_density_params.eff Parameters file to rerun find_ncs_from_density directories temp_dir= "temp_dir" Temporary work directory output_dir= "" Output directory where files are to be written density_search density_radius= 10. Radius for density to be cut out and compared peak_separation= 15 Minimum distance between centers. Use about 1.5*density_radius density_peaks= 20 Number of NCS-related peaks of density to output delta_phi= 20 Angular spacing of search ncs_copies_max= None Maximum number of NCS copies to look for min_ratio_to_top_cc= 0.75 Peaks will be kept up to ncs_copies_max, or min_ratio_to_top_cc * best cc, whichever comes first minimum_ncs_cc= 0.40 Overall NCS CC at full resolution must be at least this high dump_ncs_density= False You can dump 1 mtz file for each possible NCS copy so that you can see if the NCS is real Each file has the local map transformed to the orientation and position of copy 1 so they should all superimpose find_centers smoothing_radius= 10. Radius for smoothing squared density to find centers Choose a smaller value to get more center guesses n_center_find= None Target number of centers to find Smoothing radius will be varied from 2 to 2*smoothing_radius and the value giving the number of peaks closest to n_center_find will be used n_center_use= 1 Number of locations to consider as molecular centers in density search crystal_info resolution= 4. High-resolution limit for map calculation It is useful to cut the resolution at 3-5 A If you use higher resolution, use a finer delta_phi solvent_fraction= 0.5 solvent fraction control verbose= True Verbose output debug= False Debugging output raise_sorry= False Raise sorry if problems 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' "