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Fitting loops to fill in gaps in models with fit_loops
Author(s)
Purposefit_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. UsageHow 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_loopsmodel_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). ExamplesStandard 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=NoneThis 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=0.1To 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=TrueThis 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=TrueThis 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. Possible ProblemsSpecific limitations and problems:LiteratureAdditional informationList of all fit_loops keywords
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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
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fit_loops
input_files
pdb_in= None PDB file with gap to fill.
mtz_in= None MTZ file with coefficients for a map
map_coeff_labels= None If map coefficients cannot be identified
automatically from your MTZ file, you can specify the
label or labels for them. (Please separate labels with
blank space, MTZ columns grouped together separated by
commas with no blanks.) You can specify:
map_coeff_labels (e.g., FWT,PHIFWT) amplitudes and
phases (e.g., FP,SIGFP PHIB) or amplitudes, phases,
weights (e.g., FP,SIGFP PHIB FOM)
labin= "" Labin line for MTZ file with map coefficients. Normally use
instead map_coeff_labels. This is available for backward
compatibility. You can 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
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
skip_trim= True If skip_trim=True (default) then model with added loops
will be written out without checking for overlaps with
non-sequence-aligned residues. If skip_trim=False then this
check will be carried out. Note that skip_trim=False can
cause some residues to be de-assigned from sequence if they
cannot be successfully matched to density. In such cases you
might try skip_trim=True.
score_min= 1.0 Minimum connection score for connect_all_segments
save_acceptable_loops= False Just return a file with possible loops
n_random_loop= 200 Number of tries at building loops
connect_all_segments= False Try to connect all segments to each other,
regardless of sequence and residue numbers. Note:
this is a last-resort approach. Normally just use
the default and let fit_loops connect segments
that are close in sequence.
sequential_only= False Only connect adjacent segments in
connect_all_segments
ignore_sequence_register= False Ignore the input sequence register
all_assigned= False Assume all residues in model can be assigned to
sequence
sequence_offset= None Input sequence file residue numbers offset by
sequence_offset before use (same as adding
sequence_offset*X to beginning) Note: number of of
sequence_offset values must match number of chains in
sequence file
loop_cc_min= 0.2 Minimum loop map-model correlation
aggressive= False Aggressive loop building (risky)
target_insert= None You can try to force the number of residues to
insert with trace_loops. If none, try to fill in the gap
based on the number of missing residues. If set and
greater than 0, only accept the number of residues given.
If zero, take any length. Not supported.
loop_lib= False Use loop library to fit loops Only applicable for
chain_type=PROTEIN
standard_loops= True Use standard loop fitting
trace_loops= False Use loop tracing to fit loops Only applicable for
chain_type=PROTEIN
refine_trace_loops= True Refine loops (real-space) after trace_loops
density_of_points= None Packing density of points to consider as as
possible CA atoms in trace_loops. Try 1.0 for a quick
run, up to 5 for much more thorough run If None, try
value depending on value of quick.
max_density_of_points= None Maximum packing density of points to
consider as as possible CA atoms in trace_loops.
cutout_model_radius= None Radius to cut out density for trace_loops If
None, guess based on length of loop
max_cutout_model_radius= 20. Maximum value of cutout_model_radius to try
padding= 1. Padding for cut out density in trace_loops
max_span= 30 Maximum length of a gap to try to fill
max_overlap= None Maximum number of residues from ends to start with.
(1=use existing ends, 2=one in from ends etc) If None, set
based on value of quick.
min_overlap= None Minimum number of residues from ends to start with.
(1=use existing ends, 2=one in from ends etc)
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
gui_output_dir= None GUI use only - does not apply to command line
version
control
verbose= False Verbose output
quick= False Try to run quickly
raise_sorry= False Raise sorry if problems
debug= False Debugging output
dry_run= False Just read in and check parameter names
coarse_grid= False Use coarse grid (saves on memory)
i_ran_seed= None random seed
resolve_command_list= None Commands for resolve. One per line in the
form: keyword value value can be optional
Examples: coarse_grid resolution 200 2.0 hklin
test.mtz NOTE: for command-line usage you need to
enclose the whole set of commands in double quotes
(") and each individual command in single
quotes (') like this:
resolve_command_list="'no_build' 'b_overall
23' "
write_run_directory_to_file= None The working directory name is written
to this file
pickled_arg_dict= None Pickled keywords to __init__ are in this file
nproc= 1 You can specify the number of processors to use
max_wait_time= 1.0 You can specify the length of time (seconds) to wait
when looking for a file. If you have a cluster where jobs
do not start right away you may need a longer time to
wait. The symptom of too short a wait time is 'File not
found'
wait_between_submit_time= 1.0 You can specify the length of time
(seconds) to wait between each job that is
submitted when running sub-processes. This can
be helpful on NFS-mounted systems when running
with multiple processors to avoid file
conflicts. The symptom of too short a
wait_between_submit_time is File exists:....
background= None run jobs in background or not (if nproc is greater than
1) Usually set automatically. If run_command is sh or csh,
True
run_command= "sh " Command for running jobs (e.g., sh or qsub )
non_user_params
print_citations= True Print citation information at end of run
gui GUI-specific parameters, not used on command line
result_file= None
job_title= None Job title in PHENIX GUI, not used on command line
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