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Finding NCS from density in a map with find_ncs_from_density
Author(s)
Purposefind_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). UsageHow find_ncs_from_density works:
Output files from find_ncs_from_densityfind_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. ExamplesStandard 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 ProblemsIf 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. Specific limitations and problems:LiteratureAdditional informationList of all find_ncs_from_density keywords
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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
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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' "
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