|Python-based Hierarchical ENvironment for Integrated Xtallography|
Correlation of map and model after adjusting model for origin shifts with get_cc_mtz_pdb
get_cc_mtz_pdb is a command line tool for adjusting the origin of a PDB file using space-group symmetry so that the PDB file superimposes on a map, obtaining the correlation of model and map, and analyzing the correlation for each residue.
How get_cc_mtz_pdb works:
get_cc_mtz_pdb calculates a model map based on the supplied PDB file, then uses RESOLVE to find the origin shift (using space-group symmetry) that maximizes the correlation of this model map with a map calculated with the supplied map coefficients in an mtz file. This shift is applied to the atoms in the PDB file to create offset.pdb and then the correlation, residue-by-residue of offset.pdb with the map is analyzed. Atoms and residues that are out of density or are in weak density are flagged. You can set several parameters to define how the correlations are calculated. By default model density is calculated using the atom types, occupancies and isotropic thermal factors (B-values) supplied in the PDB file. If you specify
scale=Truethen an overall B as well as an increment in B-values for each atom beyond CB (for proteins) will be added to the values in the PDB file, after adjusting these parameters to maximize the map correlation. If you specify
use_only_refl_present_in_mtz=Truethen the model-based map will be calculated using the same set of reflections as the map calculated from your input mtz file. This reduces the contribution of missing reflections on the calculation (but the correlation is no longer the actual map-model correlation). In the calculation of the map correlation in the region of the model, the region where the model is located is defined as all points within a distance rad_max of an atom in the model. The value of rad_max is adjusted in each case to maximize this correlation. Its value is typically similar to the high-resolution limit of the map.
Output files from get_cc_mtz_pdb
Standard run of get_cc_mtz_pdb:
phenix.get_cc_mtz_pdb map_coeffs.mtz coords.pdbIf you want (or need) to specify the column names from your mtz file, you will need to tell get_cc_mtz_pdb what FP and PHIB (and optionally FOM) are, in this format:
phenix.get_cc_mtz_pdb map_coeffs.mtz coords.pdb \ labin="FP=2FOFCWT PHIB=PH2FOFCWT"
Specific limitations and problems:
In versions of PHENIX up to 1.3-final, defaults were set to maximize the correlation coefficient rather than to give the correlation using the existing thermal parameters and including only the reflections present in the mtz file. These previous defaults were equivalent to using the values:
scale=True use_only_refl_present_in_mtz=TrueThese defaults were changed so that the correlation values obtained by default in a case where no origin shifts are needed would correspond to those obtained by simply calculating (1) a map using the input map coefficients and (2) a map from the PBB file and then determining the correlation between these maps.
List of all get_cc_mtz_pdb 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 ------------------------------------------------------------------------------- get_cc_mtz_pdb pdb_in= None PDB file with coordinates to evaluate atom_selection= None Any selection specified with atom_selection is applied to input model (pdb_in) before using the model. mtz_in= None MTZ file with coefficients for a map labin= "" Labin line for MTZ file with map coefficients. This is optional if get_cc_mtz_pdb 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 offset_pdb= "offset.pdb" Output version of pdb file, offset to maximize correlation with mtz file resolution= 0. high-resolution limit for map calculation use_only_refl_present_in_mtz= False You can specify that only reflections present in your mtz file are used in the comparison. scale= False If you set scale=True then get_cc_mtz_pdb applies an overall B factor and a delta_b for each atom beyond CB. any_offset= False You can search for a match with any offset even though this is not allowed by space-group symmetry chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and side-chain atoms) temp_dir= "temp_dir" Optional temporary work directory output_dir= "" Output directory where files are to be written verbose= True Verbose output quick= False Skip the residue-by=residue correlations for a quick run raise_sorry= False Raise sorry if problems debug= False Debugging output dry_run= False Just read in and check parameter names