Fitting loops to fill in gaps in models with fit


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Fitting loops to fill in gaps in models with fit_loops

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

Author(s)

fit_loops: Tom Terwilliger

Purpose

fit_loops is a tool for building a loop into density to connect existing chain ends. You supply a model with a gap and a sequence file and coefficients for an electron density map, and you specify the first and last residues to be built. Then fit_loops will attempt to build the loop that you specify. One loop can be done at a time with fit_loops (but if you have multiple identical chains, you can fit them all at once).

You can use either of two methods to fit the loops. By default fit_loops uses resolve chain extension to try to trace residues from the ends of segments in your input PDB file. If it can connect the segments, it writes out the connecting loops. Alternatively you can use a loop library supplied with PHENIX to connect ends of segments from your input PDB file. If you want a more complete model-building process, then you will want to use phenix.autobuild . fit_loops can be run from the command line or from the PHENIX GUI.

Usage

How fit_loops works:

fit_loops calculates a map based on the supplied map coefficients, then tries to extend the ends of the supplied model into the gap region, following the electron density in the map.

Output files from fit_loops

model_with_loops.pdb: The output from fit_loops is a new PDB file containing your input model with the newly-built loop inserted into it (if a loop could be found).

Examples

Standard run of fit_loops:

A typical command-line input would be:

phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \
 seq_file=nsf.seq start=37 end=43 chain_id=None

This will fit a loop starting with residue 37 and ending with residue 43 in nsf_gap.pdb. phenix.fit_loops will expect that your existing nsf_gap.pdb model has a chain ending at residue 36 and another starting at residue 44. As chain_id=None in this example, if there are multiple chains A,B,C in nsf_gap.pdb then all 3 will be filled in. If you want (or need) to specify the column names from your mtz file, you will need to tell fit_loops what FP and PHIB (and optionally FOM) are, in this format:

phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \
 seq_file=nsf.seq start=37 end=43 chain_id=None \
labin="FP=2FOFCWT PHIB=PH2FOFCWT"

If you want to try and fit a loop with poor density, you might want to lower the threshold for the correlation of density in the loop (default minimum correlation is 0.2):

phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \
 seq_file=nsf.seq start=37 end=43 chain_id=None \
loop_cc_min=0.1

To use the loop library in PHENIX, use the keyword loop_lib:

phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \
 seq_file=nsf.seq start=37 end=39 chain_id=None loop_lib=True

This will fit a loop starting with residue 37 and ending with residue 39. The maximum current length in the loop library is 3 residues. To use the loop library in PHENIX and try to connect any pair of segments that have an geometrical relationship, use the keyword connect_all:

phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \
 seq_file=nsf.seq connect_all=True

This will go through all pairs of segments, trying to connect them with a loop from the PHENIX loop library.

Possible Problems

Specific limitations and problems:

Literature

Additional information

List of all fit_loops 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
------------------------------------------------------------------------------- 
fit_loops
   input_files
      pdb_in= None PDB file with gap to fill.
      mtz_in= None MTZ file with coefficients for a map
      labin= "" Labin line for MTZ file with map coefficients. This is
             optional if fit_loops 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
      seq_file= None sequence file (1-letter code, one copy of each chain)
      seq_prob_file= None File seq_prob.dat from resolve sequence alignment
   output_files
      pdb_out= connect.pdb Output PDB file (will be missing if no result).
      log= None Output logfile
      params_out= fit_loops_params.eff Parameters file to rerun fit_loops
   fitting
      connect_all_segments= False Try to connect everything
      min_acceptable_prob= None Minimum loop probability to consider
      refine_loops= True Refine fitted loops in loop_lib
      chain_id= None Chain ID for chain containing missing loops. If None any
                chain ID is allowed. All missing segments matching chain_id,
                start and end will be fit
      start= None Starting residue number of loop(s) to be fit. if None any
             start is allowed. All missing segments matching chain_id, start
             and end will be fit
      end= None Ending residue number of loop(s) to be fit. If None any end is
           allowed. All missing segments matching chain_id, start and end will
           be fit
      remove_loops= False Remove existing residues and replace with new loop
                    All segments matching chain_id, start and end will be fit
      score_min= 1.0 Minimum connection score for connect_all_segments
      loop_cc_min= 0.2 Minimum loop map-model correlation
      aggressive= False Aggressive loop building (risky)
      loop_lib= False Use loop library to fit loops Only applicable for
                chain_type=PROTEIN
   crystal_info
      resolution= 0. high-resolution limit for map calculation
      chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
                  side-chain atoms)
   directories
      temp_dir= "temp_dir" Optional temporary work directory
      output_dir= None Output directory where files are to be written
   control
      verbose= False Verbose output
      quick= False Try to run quickly
      debug= False Debugging output
      dry_run= False Just read in and check parameter names
   gui
      result_file= None