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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.
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.
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).
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. Note that this is a last-resort approach, normally instead use the default and let fit_loops connect segments that are close in sequence.
To specify a particular gap for loop fitting, you can say
phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \ seq_file=nsf.seq start=37 end=39 chain_id=A
Note the residue number for start and end are the first and last in the gap, not the residues flanking the gap that are already present. This command fits a gap present at residues 37-39. Note: if any of the residues from 37-39 are still present in your model, specify remove_loop=True and fit_loops will remove them (otherwise it will just fit the existing gap).
One of the most common problems is that the residues just before and after a gap are themselves poorly fitted. A solution is to remove the last couple residues before a loop and the first couple residues after the loop and to try and fit the resulting larger gap. To do this you can say something like:
phenix.fit_loops pdb_in=nsf_gap.pdb mtz_in=map_coeffs.mtz \ seq_file=nsf.seq start=35 end=41 chain_id=A replace_residues=True
Here the replace_residues=True command is required to tell fit_loops to remove residues 35 and 36 and residues 40 and 41 before trying to fit residues 35-41.
You can also accomplish this by leaving the parameter trim_ends_if_needed=True, which will do this automatically (trying several possible trimmings of the ends).
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