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 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 that maximizes the correlation of this model map with the supplied map. 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 supplied map is analyzed. Atoms and residues that are out of density or are in weak density are flagged

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 are, in this format:

phenix.get_cc_mtz_pdb map_coeffs.mtz coords.pdb \
labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT"

Possible Problems

Specific limitations and problems:

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
   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
   resolution= 0. high-resolution limit for map calculation
   chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
               side-chain atoms)
   temp_dir= "temp_dir" Optional temporary work directory (must exist if you
             specify it)
   output_dir= "" Output directory where files are to be written