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Quick model-building of a single model with resolve using build_one_model
Author(s)
PurposeIf you have an mtz map coefficients file and a sequence file, you can use build_one_model to just build a single model with resolve. You can also extend an existing model. UsageHow build_one_model works:build_one_model runs resolve model-building, by default in superquick_build mode. If you supply a model, then resolve will try to extend the ends of each chain in your model. Output files from build_one_modelbuild_one_model.pdb: A PDB file with the resulting model ExamplesStandard run of build_one_model:Running build_one_model is easy. From the command-line you can type: phenix.build_one_model map_coeffs.mtz \ sequence.dat free_in=exptl_fobs_phases_freeR_flags.mtzwhere exptl_fobs_phases_freeR_flags.mtz has your free R flags for refinement. If you want to supply a PDB file to extend instead you can do that: phenix.build_one_model map_coeffs.mtz \ sequence.dat free_in=exptl_fobs_phases_freeR_flags.mtz \ model.pdb Possible ProblemsSpecific limitations and problems:LiteratureAdditional informationList of all build_one_model 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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build_one_model
input_files
seq_file= None File with 1-letter code sequence of molecule. Chains
separated by blank line or greater-than sign
pdb_in= None Optional starting PDB file (ends will be extended if
present)
map_coeffs= None MTZ file with coefficients for a map
labin_map_coeffs= None Labin line for MTZ file with map coefficients.
This is optional if build_one_model 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
ncs_info_file= None ncs_spec file with NCS information (written by
simple_ncs_from_pdb or find_ncs)
remove_free
free_in= None MTZ file containing FreeR_flags NOTE free_in only used
in build_one_model. Ignored by phase_and_build Used as
source of freeR information for real_space refinement. Note
other columns of data may be present and can be used in
reciprocal-space refinement. A suitable file is
exptf_fobs_phases_freeR_flags.mtz from autosol/autobuild or
my_model_refine_data.mtz from phenix.refine
labin_free= None Labin line for MTZ file with FreeR_flags. This is
optional if build_one_model can guess the correct
coefficients for FreeR_flags.Otherwise specify:
FreeR_flags==myFreeR_flags
map_coeffs_no_free= None Optional MTZ file with coefficients for a
map with freeR set removed. Use instead of
free_in. This map will be used for real-space
refinement
labin_no_free= None Labin line for MTZ file with map coefficients and
freeR set removed. This is optional if build_one_model
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
output_files
pdb_out= build_one_model.pdb Output PDB file
log= build_one_model.log Output log file
params_out= build_one_model_params.eff Parameters file to rerun
build_one_model
model_building_log= model_building.log Log file for model-building
refinement
rs_refine= True You can run real-space refinement after model-building
NOTE: real_space refinement requires a source of FreeR_flag
and standard requires Fobs SigFobs and a source of FreeR_flag
For real-space refinement you can supply either an mtz file
with a FreeR_flag column or an mtz map file that has all the
FreeR reflections removed
model_building
quick= False You can run quickly (superquick_build/delta_phi=30.) or
more thoroughly (default, thorough_build/delta_phi=20.)
insert_helices= False You can find helices and use them as a starting
point for model-building. This is useful if your
resolution is worse than 3 A.
i_ran_seed= 712341 Random seed for model-building
directories
temp_dir= "temp_dir" Optional temporary work directory
output_dir= "" Output directory where files are to be written
top_output_dir= "" Top output directory for control files
crystal_info
resolution= 0. high-resolution limit for map calculation
solvent_fraction= None You can specify the solvent fraction Normally it
is set automatically
chain_type= *PROTEIN DNA RNA Chain type (for identifying main-chain and
side-chain atoms)
semet= False You can specify that your protein contains selenomethionine
control
verbose= False Verbose output
raise_sorry= False Raise sorry if problems
debug= False Debugging output
dry_run= False Just read in and check parameter names
write_run_directory_to_file= None The working directory name is written
to this file
resolve_command_list= None You can supply any resolve command here 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' "
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