Correlation of map and model after adjusting model for origin shifts with get_cc_mtz


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Correlation of map and model after adjusting model for origin shifts with get_cc_mtz_pdb

Author(s)
Purpose
Usage: How get_cc_mtz_pdb works:; Output files from get_cc_mtz_pdb
Examples: Standard run of get_cc_mtz_pdb:
Possible Problems: Specific limitations and problems:
Literature
Additional information: List of all get_cc_mtz_pdb keywords

Author(s)

get_cc_mtz_pdb: Tom Terwilliger

Purpose

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.

Usage

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=True

then 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=True

then 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

offset.pdb: A PDB file offset to match the origin in the mtz file.

Examples

Standard run of get_cc_mtz_pdb:

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

phenix.get_cc_mtz_pdb map_coeffs.mtz coords.pdb

If 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"

Possible Problems

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=True

These 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.

Literature

Additional information

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" Temporary work directory
   output_dir= "" Output directory where files are to be written
   gui_output_dir= None
   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
   job_title= None Job title in PHENIX GUI, not used on command line