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Automated Model Building and Rebuilding using AutoBuild
Author(s)
PurposePurpose of the AutoBuild WizardThe purpose of the AutoBuild Wizard is to provide a highly automated system for model rebuilding and completion. The Wizard design allows the user to specify data files and parameters through an interactive GUI, or alternatively through keyworded scripts. The AutoBuild Wizard begins with datafiles with structure factor amplitudes and uncertainties, along with either experimental phase information or a starting model, carries out cycles of model-building and refinement alternating with model-based density modification, and producing a relatively complete atomic model. The AutoBuild Wizard uses RESOLVE, (optionally also TEXTAL), xtriage and phenix.refine to build an atomic model, refine it, and improve it with iterative density modification, refinement, and model-building The Wizard begins with either experimental phases (i.e., from AutoSol) or with an atomic model that can be used to generate calculated phases. The AutoBuild Wizard produces a refined model that can be nearly complete if the data are strong and the resolution is about 2.5 A or better. At lower resolutions (2.5 - 3 A) the model may be less complete and at resolutions > 3A the model may be quite incomplete and not well refined. The AutoBuild Wizard can be used to generate OMIT maps (simple omit, SA-omit, iterative-build omit) that can cover the entire unit cell or specific residues in a PDB file. The AutoBuild Wizard can generate a set of models compatible with experimental data (multiple_models) UsageThe AutoBuild Wizard can be run from the PHENIX GUI, from the command-line, and from keyworded script files. All three versions are identical except in the way that they take commands from the user. See Running a Wizard from a GUI, the command-line, or a script for details of how to run a Wizard. The command-line version will be described here. How the AutoBuild Wizard worksThe AutoBuild Wizard begins with experimental structure factor amplitudes, along with either experimental or model-based estimates of crystallographic phases. The phase information is improved by using statistical density modification to improve the correlation of NCS-related density in the map (if present) and to improve the match of the distribution of electron densities in the map with those expected from a model map. This improved map is then used to build and refine an atomic model. In subsequent cycles, the models from previous cycles are used as a source of phase information in statistical density modification, iteratively improving the quality of the map used for model-building. Additionally, during the first few cycles additional phase information is obtained by detecting and enhancing (1) the presence of commonly-found local patterns of density in the map, and (2) the presence of density in the shape of helices and strands. The final model obtained is analyzed for residue-based map correlation and density at the coordinates of individual atoms, and an analysis including a summary of atoms and residues that are in strong, moderate, or weak density and out of density is provided. Automation and user controlThe AutoBuild Wizard has been designed for ease of use combined with maximal user control, with as many parameters set automatically by the Wizard as possible, but maintaining parameters accessible to the user through a GUI and through keyword-based scripts. The Wizard uses the input/output routines of the cctbx library, allowing data files of many different formats so that the user does not have to convert their data to any particular format before using the Wizard. Use of the phenix.refine refinement package in the AutoBuild Wizard allows a high degree of automation of refinement so that the neither user nor Wizard is required to specify parameters for refinement. The phenix.refine package automatically includes a bulk solvent model and automatically places solvent molecules. Core modules in the AutoBuild WizardThe five core modules in the AutoBuild Wizard are
The standard procedures available in the AutoBuild Wizard that are based on these modules include:
Starting from a set of experimental phases and structure factor amplitudes, normally procedure (a) is carried out, and then the resulting model is rebuilt with procedure (b). Starting from a model (e.g., from molecular replacement) and experimental structure factor amplitudes, procedure (c) is normally carried out if the starting model differs less than about 50% in sequence from the desired model, and otherwise procedure (b) is used. How to run the AutoBuild WizardRunning the AutoBuild Wizard is easy. For example, from the command-line you can type: phenix.autobuild data=w1.sca seq.dat model=coords.pdb The AutoBuild Wizard will carry out iterative model-building, density modification and refinement based on the data in w1.sca and the model in coords.pdb, editing the model as necessary to match the sequence in seq.dat. What the AutoBuild wizard needs to run
...and optional files
Specifying which columns of data to use from input data filesIf one or more of your data files has column names that the Wizard cannot identify automatically, you can specify them yourself. You will need to provide one column "name" for each expected column of data, with "None" for anything that is missing. For example, if your data file ref.mtz has columns FP SIGFP and FreeR then you might specify refinement_file=ref.mtz input_refinement_labels="FP SIGFP None None None None None None FreeR" The keywords for labels and anticipated input labels (program labels) are: input_labels (for data file): FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR_flag input_refinement_labels: FP SIGFP FreeR_flag input_map_labels: FP PHIB FOM input_hires_labels: FP SIGFP FreeR_flag You can find out all the possible label strings in a data file that you might use by typing: phenix.autosol display_labels=w1.mtz # display all labels for w1.mtz NOTES: if your data files contain a mixture of amplitude and intensity data then only the amplitude data is available. If you have only intensity data in a data file and want to select specific columns, then you need to specify the column names as they are after importing the data and conversion to amplitudes (see below under General Limitations for details). Specifying other general parametersYou can specify many more parameters as well. See the list of keywords, defaults and descriptions at the end of this page and also general information about running Wizards at Running a Wizard from a GUI, the command-line, or a script for how to do this. Some of the most common parameters are: data=w1.sca # data file model=coords.pdb # starting model seq_file=seq.dat # sequence file map_file=map_coeffs.mtz # coefficients for a starting map for building resolution=3 # dmin of 3 A s_annealing=True # use simulated annealing refinement at start of each cycle n_cycle_build_max=5 # max number of build cycles (starting from experimental phases) n_cycle_rebuild_max=5 # max number of rebuild cycles (starting from a model) Picking waters in AutoBuildBy default AutoBuild will instruct phenix.refine to pick waters using its standard procedure. This means that if the resolution of the data is high enough (typically 3 A) then waters are placed. You can tell AutoBuild not to have phenix.refine pick waters with the command: place_waters=FalseIf you want to place waters at a lower resolution, you will need to reset the low-resolution cutoff for placing waters in phenix.refine. You would do that in a "refinement_params.eff" file containing lines like these (see below for passing parameters to phenix.refine with an ".eff" file): refinement {
ordered_solvent {
low_resolution = 2.8
}
}
Keeping waters from your input file in AutoBuildYou can tell AutoBuild to keep the waters in your input file when you are using rebuild_in_place (the default is to toss them and replace them with new ones). You can say, keep_input_waters=True place_waters=NoNOTE: If you specify keep_input_waters=True you should also specify either "place_waters=No" or "keep_pdb_atoms=No" . This is because if place_waters=Yes and keep_pdb_atoms=Yes then phenix.refine will add waters and then the wizard will keep the new waters from the new PDB file created by phenix.refine preferentially over the ones in your input file. Specifying phenix.refine parametersYou can control phenix.refine parameters that are not specified directly by AutoBuild using a refinement parameters (.eff) file: refine_eff_file=refinement_params.eff # set any phenix.refine params not set by AutoBuildThis file might contain a twin-law for refinement: refinement {
twinning {
twin_law = "-k, -h, -l"
}
}
You can put any phenix.refine parameters in this file, but a few parameters that are set directly by AutoBuild override your inputs from the refine_eff_file. These parameters are listed below. Refinement parameters that must be set using AutoBuild Wizard keywords (overwriting any values provided by user in input_eff_file) The following parameters controlling phenix.refine output are set directly in AutoBuild and cannot be set by the user
Specifying resolve/resolve_pattern parametersSimilarly, you can control resolve and resolve_pattern parameters. For these parameters, your inputs will not be overridden by AutoBuild. The format is a little tricky: you have to put two sets of quotes around the command like this: resolve_command="'resolution 200 3'" # NOTE ' and " quotesThis will put the text resolution 200 3at the end of every temporary command file created to run resolve. (This is why it is not overridden by AutoBuild commands; they will all come before your commands in the resolve command file.) Note that some commands in resolve may be incompatible with this usage. Including ligand coordinates in AutoBuildIf your input PDB file contains ligands (anything other than solvent that is not protein if your chain_type=PROTEIN, for example) then by default these ligands will be kept, used in refinement, and written out to your output PDB file. Any solvent molecules will by default be discarded. You can change this behavior by changing the keywords from these defaults: keep_input_ligands=True keep_input_waters=FalseThe AutoBuild Wizard will use phenix.elbow to generate geometries for any ligands that are not recognized. You can also tell AutoBuild to add the contents of any PDB files that you wish to supply to the current version of the structure just before refinement, so all the refined models produced contain whatever AutoBuild has built, plus the contents of these PDB files. This can be done through the GUI, the command-line, or a script. In the command-line version you do this with: input_lig_file_list=my_ligand.pdb NOTE: The files in input_lig_file_list will be edited to make them all HETATM records to tell AutoBuild to ignore these residues in rebuilding. NOTE You may need to tell phenix.refine about the geometry of your ligands. You will get an error message if the ligand is not recognized and an automatic run of phenix.elbow does not succeed in generating your ligand. In that case you will want to run phenix.elbow to create a cif definition file for this ligand: phenix.elbow my_ligand.pdb --id=LIGwhere LIG is the 3-letter ID code that you use in my_ligand.pdb to identify your ligand. If the automatic run does not work you may need to give phenix.elbow additional information to generate your ligand. Once phenix.elbow has generated your ligand you can use the keyword "cif_def_file_list" to tell AutoBuild about this ligand: cif_def_file_list=elbow.LIG.my_ligand.pdb.cif Specifying arbitrary commands and cif files for phenix.refineYou can tell AutoBuild to apply any set of cif definitions to the model during refinement by using a combination of specification files and the commands cif_def_file_list and refine_eff_file_list: refine_eff_file_list=link.eff cif_def_file_list=link.cifThis example comes from the phenix.refine manual page in which a link is specified in a cif definition file link.cif: data_mod_5pho # loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 5pho add . O5T O OH . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 5pho add O5T P coval 1.520 0.020 and this is applied with a parameters file link.eff: refinement.pdb_interpretation.apply_cif_modification
{
data_mod = 5pho
residue_selection = resname GUA and name O5T
}
You can have any number of cif files and parameters files. Output files from AutoBuildWhen you run AutoBuild the output files will be in a subdirectory with your run number: AutoBuild_run_1_/ # subdirectory with results
Standard building, rebuild_in_place, and multiple-modelsThe AutoBuild Wizard has two overall methods for building a model. The first method (standard build) is to build a model from scratch. This involves identification of where helices (and strands, for proteins) are located, extension using fragment libraries, connection of segments, identification of side-chains, and sequence alignment. These methods are augmented in the standard building procedure by loop-fitting and building model outside of the region that has already been built. The second method (rebuild_in_place) takes an existing model and rebuilds it without adding or deleting any residues and without changing the connectivity of the chain. The way this works is a segment of the model is deleted and then is filled-in again by rebuilding from the remaining ends. This is repeated for overlapping segments covering the entire model. The multiple-models approach really has two levels of multiple models. At the first level, several (multiple_models_group_number, default is number_of_parallel_models) models are built (using rebuild_in_place) and are then recombined into a single good model. At the next level, this whole process may be done more than once (multiple_models_number times), yielding several very good models. By default, if you ask for rebuild_in_place, then you will get a single very good model, created by running rebuild_in_place several times and recombining the models. Parallel jobs, nproc, nbatch, number_of_parallel_models and how AutoBuild works in parallelThe AutoBuild Wizard is set up to take advantage of multi-processor machines or batch queues by splitting the work into separate tasks. See Tutorial 4: Iterative model-building, density modification and refinement starting from experimental phases and Tutorial 6: Automatically rebuilding a structure solved by Molecular Replacement for a description of the method used by the AutoBuild Wizard to run build jobs as sub-processes and to combine the results into single models. Here are the key factors that determine how splitting model-building into batches and running them on one or more processors works:
Model editing during rebuilding with the Coot-PHENIX interfaceThe AutoBuild Wizard allows you to edit a model and give it back to the Wizard during the iterative model-building, density modification and refinement process. The Wizard will consider the model that you give it along with the models that it generates automatically, and will choose the parts of your model that fit the density better than other models. You can edit a model using the PHENIX-Coot interface. This interface is accessible through the GUI and via the command-line. Using the GUI, when a model has been produced by the AutoBuild Wizard, you can double-click the button on the GUI labelled View/edit files with coot to start Coot with your current map and model. If you are running from the command-line, you can open a new window and type: phenix.autobuild cootwhich will do the same (provided the necessary map and model are ready). When Coot has been loaded, your map and model will be displayed along with a PHENIX-Coot Interface window. You can edit your model and then save it, giving it back to PHENIX with the button labelled something like Save model as COMM/overall_best_coot_7.pdb. This button creates the indicated file and also tells PHENIX to look for this file and to try and include the contents of the model in the building process. The precise use of the model that you save depends on the type of model-building that is being carried out by the AutoBuild Wizard. If you are using rebuild_in_place then the main-chain and side-chains of the model are considered as replacements for the current working model. Any ligands or unrecognized residues are (by default) not rebuilt but are included in refinement. By default, solvent in the model is ignored. If you are not using rebuild_in_place, only the main-chain conformation is considered, and the side-chains are ignored. Ligands (but not solvent) in the model are (by default) kept and included in refinement. As the AutoBuild Wizard continues to build new models and create new maps, you can update in the PHENIX-Coot Interface to the current best model and map with the button Update with current files from PHENIX. Resolution limits in AutoBuildThere are several resolution limits used in AutoBuild. You can leave them all to default, or you can set any of them individually. Here is a list of these limits and how their default values are set: ExamplesRun AutoBuild automatically after AutoSolphenix.autobuild after_autosol Run AutoBuild beginning with experimental dataphenix.autobuild data=solve_1.mtz seq_file=seq.dat Merge in hires dataphenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat Make a SA-omit map around atoms in target.pdbphenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omitCoefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). Make a simple composite omit mapphenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=simple_omitCoefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). Make an iterative-build omit map around atoms in target.pdbphenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \ composite_omit_type=iterative_build_omitCoefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). Make a sa-omit map around residues 3 and 4 in chain A of coords.pdbphenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=coords.pdb \ omit_res_start_list=3 omit_res_end_list=4 omit_chain_list=A \ composite_omit_type=sa_omitCoefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note 1: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz). (Note 2: Although the variables are omit_res_start_list omit_res_end_list omit_chain_list, you can only specify one region of a molecule to omit, not a list of them, all others are ignored.) Create one very good rebuilt modelphenix.autobuild data=data.mtz model=coords.pdb multiple_models=True \ include_input_model=True \ multiple_models_number=1 n_cycle_rebuild_max=5The final model will be in the file MULTIPLE_MODELS/all_models.pdb (this file will contain just one model). Note that this procedure will keep the sequence that is present in coords.pdb. If you supply a sequence file it will edit the sequence of coords.pdb to match your sequence file and discard any residues that do not match. (If you want to input a sequence file but not edit the sequence in coords.pdb and not discard any non-matching residues, then specify also edit_pdb=False.) Note also that if include_input_model=True then no randomization cycle will be carried out and multiple_models_starting_resolution is ignored. Touch up a modelphenix.autobuild data=data.mtz model=coords.pdb \ touch_up=True worst_percent_res_rebuild=2 min_cc_res_rebuild=0.8You can rebuild just the worst parts of your model by settting touch_up=True. You can decide what parts to rebuild based on a minimum model-map correlation (by residue). You can decide how much to rebuild using worst_percent_res_rebuild or with min_cc_res_rebuild, or both. Create 20 very good rebuilt models that are as different as possiblephenix.autobuild data=data.mtz model=coords.pdb multiple_models=True \ multiple_models_number=20 n_cycle_rebuild_max=5The 20 models will be in the file MULTIPLE_MODELS/all_models.pdb. This procedure is useful for generating an ensemble of models that are each individually consistent with the data, and yet are diverse. The variation among these models is an indication of the uncertainty in each of the models. Note that the ensemble of models is not a representation of the ensemble of structures that is truly present in the crystal. Build an RNA chainphenix.autobuild data=solve_1.mtz seq_file=seq.dat chain_type=RNA Build a DNA chainphenix.autobuild data=solve_1.mtz seq_file=seq.dat chain_type=DNA Just make maps; don't do any building.phenix.autobuild data=data.mtz model=coords.pdb maps_only=True Just calculate a prime-and-switch mapphenix.autobuild data=data.mtz solvent_fraction=.6 \ ps_in_rebuild=True model=coords.pdb maps_only=TrueThe output prime-and-switch map will be in the file prime_and_switch.mtz. Possible ProblemsGeneral limitations
Specific limitations and problems
Literature
Additional informationList of all AutoBuild 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
-------------------------------------------------------------------------------
autobuild
write_run_directory_to_file= None Writes the full name of a run directory
to the specified file. This can be used as a
call-back to tell a script where the output is
going to go. (Command-line only)
coot= None Set coot to True and optionally run=[run-number] to run Coot
with the current model and map for run run-number. In some wizards
(AutoBuild) you can edit the model and give it back to PHENIX to use
as part of the model-building process. If you just say coot then the
facts for the highest-numbered existing run will be shown.
(Command-line only)
ignore_blanks= None ignore_blanks allows you to have a command-line keyword
with a blank value like "input_lig_file_list="
stop= None You can stop the current wizard with "stopwizard" or "stop". If
you type "phenix.autobuild run=3 stop" then this will stop run 3 of
autobuild. (Command-line only)
display_facts= None Set display_facts to True and optionally
run=[run-number] to display the facts for run run-number. If
you just say display_facts then the facts for the
highest-numbered existing run will be shown. (Command-line
only)
display_summary= None Set display_summary to True and optionally
run=[run-number] to show the summary for run run-number.
If you just say display_summary then the summary for the
highest-numbered existing run will be shown. (Command-line
only)
carry_on= None Set carry_on to True to carry on with highest-numbered run
from where you left off. (Command-line only)
run= None Set run to n to continue with run n where you left off.
(Command-line only)
copy_run= None Set copy_run to n to copy run n to a new run and continue
where you left off. (Command-line only)
display_runs= None List all runs for this wizard. (Command-line only)
delete_runs= None List runs to delete: 1 2 3-5 9:12 (Command-line only)
display_labels= None display_labels=test.mtz will list all the labels that
identify data in test.mtz. You can use the label strings
that are produced in AutoSol to identify which data to use
from a datafile like this: peak.data="F+ SIGF+ F- SIGF-" #
the entire string in quotes counts here You can use the
individual labels from these strings as identifiers for
data columns in AutoSol and AutoBuild like this:
input_refinement_labels="FP SIGFP FreeR_flags" # each
individual label counts
dry_run= False Just read in and check parameter names
data= None Datafile (alias for input_data_file) This file can be a .sca or
mtz or other standard file. The Wizard will guess the column
identification. You can specify the column labels to use with:
input_labels='FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR_flag'
Substitute any labels you do not have with None. If you only have
myFP and mysigFP you can just say input_labels='myFP mysigFP'.
(Command-line only)
model= None PDB file with starting model (alias for input_pdb_file) NOTE:
If your PDB file has been previously refined, then please make sure
that you provide the free R flags that were used in that refinement.
These can come from the data file or from the refinement_file.
(Command-line only).
seq_file= Auto Sequence file (alias for input_seq_file). The format is
plain text, with chains separated by >>>: >>>
any text here ignored, next lines are sequence; any blanks
ignored galmtdeqr ragwqst >>> indicate new chain with
'>>>' asqrarpt >>> input 1 copy of each unique
chain. (Command-line only)
map_file= Auto MTZ file containing starting map (alias for input_map_file)
This file must be a mtz file. The Wizard will guess the column
identification. You can specify the column labels to use with:
input_map_labels='FP PHIB FOM' Substitute any labels you do not
have with None. If you only have myFP and myPHIB you can just say
input_map_labels='myFP myPHIB'. (Command-line only)
refinement_file= Auto File for refinement (alias for input_refinement_file)
This file can be a .sca or mtz or other standard file.
This file will be merged with your data file, with any
phase information coming from your data file. If this file
has free R flags, they will be used, otherwise if the data
file has them, those will be used, otherwise they will be
generated. The Wizard will guess the column
identification. You can specify the column labels to use
with: input_refinement_labels='FP SIGFP FreeR_flag'
Substitute any labels you do not have with None. If you
only have myFP and mysigFP you can just say
input_refinement_labels='myFP mysigFP'. (Command-line
only).
hires_file= Auto File with high-resolution data (alias for
input_hires_file) This file can be a .sca or mtz or other
standard file. The Wizard will guess the column identification.
You can specify the column labels to use with:
input_hires_labels='FP SIGFP'. (Command-line only)
acceptable_r= 0.25 Used to decide whether the model is acceptable enough to
quit if it is not improving much. A good value is 0.25
after_autosol= Yes *No True False You can specify that you want to continue
on starting with the highest-scoring run of AutoSol.
allow_negative_residues= Yes *No True False Normally the wizard does not
allow negative residue numbers, and all residues
with negative numbers are rejected when they are
read in. You can allow them if you wish.
background= *Yes No True False When you specify nproc=nn, you can run the
jobs in background (default if nproc is greater than 1) or
foreground (default if nproc=1). If you set run_command=qsub
(or otherwise submit to a batch queue), then you should set
background=False, so that the batch queue can keep track of
your runs. There is no need to use background=True in this case
because all the runs go as controlled by your batch system. If
you use run_command=csh (or similar, csh is default) then
normally you will use background=True so that all the jobs run
simultaneously.
background_map= None You can supply an mtz file (REQUIRED LABELS: FP PHIM
FOMM) to use as map coefficients to calculate the electron
density in all points in an omit map that are not part of
any omitted region. (Default="")
boundary_background_map= None You can supply an mtz file (REQUIRED LABELS:
FP PHIM FOMM) to use as map coefficients to
calculate the electron density in all points in
the boundary map that are not part of any omitted
region. (Default="")
build_outside= *Yes No True False Define whether to use the BuildOutside
module in build_model
build_type= RESOLVE_AND_TEXTAL *RESOLVE TEXTAL You can choose to build
models with RESOLVE and TEXTAL or either one, and how many
different models to build with RESOLVE. The more you build, the
more likely to get a complete model. Note that rebuild_in_place
can only be carried out with RESOLVE model-building
cell= 0.0 0.0 0.0 0.0 0.0 0.0 Enter cell parameter a b c alpha beta gamma
chain_type= *Auto PROTEIN DNA RNA You can specify whether to build protein,
DNA, or RNA chains. At present you can only build one of these
in a single run. If you have both DNA and protein, build one
first, then run AutoBuild again, supplying the prebuilt model
in the "input_lig_file_list" and build the other. NOTE: default
for this keyword is Auto, which means "carry out normal process
to guess this keyword". The process is to look at the sequence
file and/or input pdb file to see what the chain type is. If
there are more than one type, the type with the larger number
of residues is guessed. If you want to force the chain_type,
then set it to PROTEIN RNA or DNA.
cif_def_file_list= None You can enter any number of CIF definition files.
These are normally used to tell phenix.refine about the
geometry of a ligand or unusual residue. You usually
will use these in combination with "PDB file with
metals/ligands" (keyword "input_lig_file_list" ) which
allows you to attach the contents of any PDB file you
like to your model just before it gets refined. You can
use phenix.elbow to generate these if you do not have a
CIF file and one is requested by phenix.refine
clean_up= Yes *No True False At the end of the entire run the TEMP
directories will be removed if clean_up is True. The default is
No, keep these directories. If you want to remove them after your
run is finished use a command like "phenix.autobuild run=1
clean_up=True"
combine_only= Yes *No True False Once you have created a set of initial
models you can merge them together into a final set. This
option is useful if you have split up the creation of
multiple models into different directories, and then you have
copied all the initial models to one directory for combining.
composite_omit_type= *None simple_omit sa_omit iterative_build_omit Your
choices of types of OMIT maps are: None - normal
operation, no omit simple_omit - omit the atoms in
OMIT region in calculating a sigmaA-weighted 2mFo-DFc
map with no refinement sa_omit - omit the atoms in
OMIT region, carry out simulated-annealing refinement,
then calculate a sigmaA-weighted 2mFo-DFc map.
iterative_build_omit - set occupancy of atoms in OMIT
region to 0 throughout an entire iterative
model-building, density modification and refinement
process (takes a long time). All these omit map types
are available as composite omit maps (default) or as
omit maps around a region defined by a PDB file (using
omit_box_pdb_list) The resulting OMIT map will be in
the directory OMIT with file name
resolve_composite_map.mtz . This mtz file contains the
map coefficients to create the OMIT map. The file
"omit_region.mtz" contains the coefficients for a map
showing the boundaries of the OMIT region.
connect= *Yes No True False Define whether to use the connect module in
build_model. This module tries to connect nearby chains with
loops, without using the sequence. This is different than
fit_loops (which uses the sequence to identify the exact number of
residues in the loop).
consider_main_chain_list= None This keyword lets you name any number of PDB
files to consider as templates for
model-building. Every time models are built, the
contents of these files will be merged with them
and the best parts will be kept. NOTE: this only
uses the main-chain atoms of your PDB files.
coot_name= coot If your version of coot is called something else, then you
can specify that here.
d_max_textal= 1000.0 This low-resolution limit is only used for Textal
model-building
d_min_textal= 2.8 Textal has an optimal high-resolution limit of 2.8 A This
limit is only used for Textal model-building
debug= Yes *No True False You can have the wizard stop with error messages
about the code if you use debug. NOTE: you cannot use Pause with
debug.
dist_close= None If main-chain atom rmsd is less than dist_close then
crossover between chains in different models is allowed at this
point. If you input a negative number the defaults will be used
dist_close_overlap= 1.5 Model or ligand coordinates but not both are kept
when model and ligand coordinates are within
dist_close_overlap and ligands in input_lig_file_list
are being added to the current model. NOTE: you might
want to decrease this if your ligand atoms get removed
by the wizard. Default=1.5 A
dmax= 500.0 Low-resolution limit
edit_pdb= *Yes No True False You can choose to edit the input PDB file in
rebuild_in_place to match the input sequence (default=True).
NOTE: residues with residue numbers higher than 'highest_resno'
are assumed to not have a known sequence and will not be edited.
By default the value of 'highest_resno' is the highest residue
number from the sequence file, after adding it to the starting
residue number from start_chains_list. You can also set it
directly
extend_try_list= None You can fill out the list of parallel jobs to match
the number of jobs you want to run at one time, as
specified with nbatch.
extensive_build= Yes *No True False You can choose whether to build a new
model on every cycle and carry out extra model-building
steps every cycle. Default is No (build a new model on
first cycle, after that carry out extra steps).
extra_verbose= Yes *No True False Facts and possible commands will be
printed every cycle if Yes
find_ncs= *Auto Yes No True False This script normally deduces ncs
information from the NCS in chains of models that are built
during iterative model-building. The update is done each cycle in
which an improved model is obtained. Say No to skip this. See
also "input_ncs_file" which can be used to specify NCS at the
start of the process. If find_ncs="No" then only this starting
NCS will be used and it will not be updated. You can use find_ncs
"No" to specify exactly what residues will be used in NCS
refinement and exactly what NCS operators to use in density
modification. You can use the function
$PHENIX/phenix/phenix/command_line/simple_ncs_from_pdb.py to help
you set up an input_ncs_file that has your specifications in it.
fit_loops= *Yes No True False You can fit loops automatically if sequence
alignment has been done.
group_ca_length= 4 In resolve building you can specify how short a fragment
to keep. Normally 4 or 5 residues should be the minimum.
group_length= 2 In resolve building you can specify how many fragments must
be joined to make a connected group that is kept. Normally 2
fragments should be the minimum.
helices_strands_only= Yes *No True False You can choose to use a quick
model-building method that only builds secondary
structure. At low resolution this may be both quicker
and more accurate than trying to build the entire
structure If you are running the AutoSol Wizard,
normally you should choose 'Yes' and use the quick
model-building. Then when your structure is solved by
AutoSol, go on to AutoBuild and build a more complete
model (this time normally using
helices_strands_only=False).
highest_resno= None Highest residue number to be considered "placed" in
sequence for rebuild_in_place
hl= Yes *No True False You can choose whether to calculate hl coeffs when
doing density modification ('Yes') or not to do so ('No'). Default is
No.
i_ran_seed= 289564 Random seed (positive integer) for model-building and
simulated annealing refinement
include_input_model= *Yes No True False The keyword include_input_model
defines whether the input model (if any) is to be
crossed with models that are derived from it, and the
best parts of each kept. Note that if
multiple_models=True and include_input_model=True then
no initial cycle of randomization will be carried out
and the keyword multiple_models_starting_resolution is
ignored. In most cases you should use
include_input_model=True If you want to generate
maximum diversity with multiple-models then you may
wish to use include_input_model=False. Also if you
want to decrease the amount of bias from your starting
model you may wish to use include_input_model=False.
include_molprobity= Yes *No True False You can choose to include the clash
score from MolProbity as one of the scoring criteria in
comparing and merging models. The score is combined
with the model-map correlation CC by summing in a
weighted clashscore. If clashscore for a residue has a
value < ok_molp_score then its value is
(clashscore-ok_molp_score)*scale_molp_score, otherwise
its value is zero.
input_compare_file= NONE If you are rebuilding a model or already think you
know what the model should be, you can include a
comparison file in rebuilding. The model is not used
for anything except to write out information on
coordinate differences in the output log files. NOTE:
this feature does not always work correctly.
input_data_file= None Enter the a file with input structure factor data.
For structure factor data only (e.g., FP SIGFP) any format
is ok. If you have free R flags, phase information or HL
coefficients that you want to use then an mtz file is
required. If this file contains phase information, this
phase information should be experimental (i.e.,
MAD/SAD/MIR etc), and should not be density-modified
phases (enter any files with density-modified phases as
input_map_file instead). If you also specify a hires data
file, then FP and SIGFP will come from that data file (and
not this one) If an input_refinement_file is specified,
then F, Sigma, FreeR_flag (if present) from that file will
be used for refinement instead of this one.
input_ha_file= None If the flag "truncate_ha_sites_in_resolve" is set then
density at sites specified with input_ha_file is truncated
to improve the density modification procedure.
input_hires_labels= None Labels for input hires file (FP SIGFP FreeR_flag)
input_labels= None Labels for input data columns NOTE: Applies to input
data file for LigandFit and AutoBuild, but not to AutoMR. For
AutoMR use instead 'input_label_string'.
input_lig_file_list= None This script adds the contents of these PDB files
to each model just prior to refinement. Normally you
might use this to put in any heavy-atoms that are in
the refined structure (for example the heavy atoms
that were used in phasing), or to add a ligand to your
model. If the atoms in this PDB file are not
recognized by phenix.refine, then you can specify
their geometries with a cif definitions file using the
keyword "cif_def_files_list". You can easily generate
cif definitions for many ligands using phenix.elbow in
PHENIX. You can put anything you like in the files in
input_lig_file_list, but any atoms that fall within
1.5 A of any atom in the current model will be tossed
(not written to the model).
input_map_file= Auto Enter an mtz file with coefficients for map (if
different file or different coefficients than input
structure factor data ). This map will be used in the first
cycle of model-building. NOTE: default for this keyword is
Auto, which means "carry out normal process to guess this
keyword". This means if you specify "after_autosol" in
AutoBuild, AutoBuild will automatically take the value from
AutoSol. If you do not want this to happen, you can specify
None which means "No file"
input_map_labels= None Labels for input map coefficient columns (FP PHIB
FOM) NOTE: FOM is optional (set to None if you wish)
input_ncs_file= None You can enter NCS information in 3 ways: (1) an
ncs_spec file produced by AutoSol or AutoBuild with NCS
information (2) a heavy-atom PDB file that contains ncs in
the heavy-atom sites (3) a PDB file with a model that
contains chains with NCS The wizard will derive NCS
information from any of these if specified. See also
"find_ncs" which determines whether the wizard will update
NCS from models that are built during iterative building.
input_pdb_file= None You can enter a PDB file containing a starting model
of your structure NOTE: If you enter a PDB file then the
AutoBuild wizard will start right in with rebuild steps,
skipping the build process. If the model is very poor than
it may be better to leave it out as the build process
(which includes pattern recognition and recognition of
helical and strand fragments) is optimized for improving
poor maps, while the rebuild process is optimized for
better maps that can be produced by having a partial model.
input_refinement_file= Auto Data file to use for refinement. The data in
this file should not be corrected for anisotropy. It
will be combined with experimental phase information
(if any) from input_data_file for refinement. If you
leave this blank, then the data in the
input_data_file will be used in refinement. If no
anisotropy correction is applied to the data you do
not need to specify a datafile for refinement. If an
anisotropy correction is applied to the data files,
then you should enter an uncorrected datafile for
refinement. Any standard format is fine; normally
only F and sigF will be used. Bijvoet pairs and
duplicates will be averaged. If an mtz file is
provided then a free R flag can be read in as well.
Any HL coeffs and phase information in this file is
ignored. NOTE: default for this keyword is Auto,
which means "carry out normal process to guess this
keyword". This means if you specify "after_autosol"
in AutoBuild, AutoBuild will automatically take the
value from AutoSol. If you do not want this to
happen, you can specify None which means "No file"
input_refinement_labels= None Labels for input refinement file columns (FP
SIGFP FreeR_flag)
input_seq_file= Auto Enter name of file with 1-letter code of protein
sequence NOTES: 1. lines starting with >>> are
ignored and separate chains 2. FASTA format is fine 3. If
there are multiple copies of a chain, just enter one copy.
4. If you enter a PDB file for rebuilding and it has the
sequence you want, then the sequence file is not necessary.
NOTE: You can also enter the name of a PDB file that
contains SEQRES records, and the sequence from the SEQRES
records will be read, written to
seq_from_seqres_records.dat, and used as your input
sequence. NOTE: for AutoBuild you can specify
start_chains_list on the first line of your sequence file:
>>> start_chains_list 23 11 5 NOTE: default for
this keyword is Auto, which means "carry out normal process
to guess this keyword". This means if you specify
"after_autosol" in AutoBuild, AutoBuild will automatically
take the value from AutoSol. If you do not want this to
happen, you can specify None which means "No file"
keep_input_ligands= *Yes No True False You can choose whether to (by
default) let the wizard keep ligands by separating them
out from the rest of your model and adding them back to
your rebuilt model, or alternatively to remove all
ligands from your input pdb file before
rebuild_in_place.
keep_input_waters= Yes *No True False You can choose whether to keep input
waters (solvent) when using rebuild_in_place. If you
keep them, then you should specify either
"place_waters=No" or "keep_pdb_atoms=No" because if
place_waters=Yes and keep_pdb_atoms=Yes then
phenix.refine will add waters and then the wizard will
keep the new waters from the new PDB file created by
phenix.refine preferentially over the ones in your input
file.
keep_pdb_atoms= *Yes No True False You can choose whether to keep the model
coordinates when model and ligand coordinates are within
dist_close_overlap and ligands in input_lig_file_list are
being added to the current model. Default=Yes
link_distance_cutoff= 3.0 You can specify the maximum bond distance for
linking residues in phenix.refine called from the
wizards.
loop_cc_min= 0.4 You can specify the minimum correlation of density from a
loop with the map.
maps_only= Yes *No True False You can choose whether to skip all
model-building and just calculate maps and write out the
results. This also runs just 1 cycle and turns on HL
coefficients.
mask_type= *histograms probability wang Choose method for obtaining
probability that a point is in the protein vs solvent region.
Default is "histograms". If you have a SAD dataset with a heavy
atom such as Pt or Au then you may wish to choose "wang" because
the histogram method is sensitive to very high peaks. Options
are: histograms: compare local rms of map and local skew of map
to values from a model map and estimate probabilities. This one
is usually the best. probability: compare local rms of map to
distribution for all points in this map and estimate
probabilities. In a few cases this one is much better than
histograms. wang: take points with highest local rms and define
as protein.
max_occ= None You can choose to set the maximum value of occupancy for
atoms that have their occupancies refined. Default is None (use
default value of 1.0 from phenix.refine)
max_wait_time= 100.0 You can specify the length of time (seconds) to wait
when testing the run_command. If you have a cluster where
jobs do not start right away you may need a longer time to
wait.
min_cc_res_rebuild= 0.5 You can rebuild just the worst parts of your model
by settting touch_up=True. You can decide what parts to
rebuild based on a minimum model-map correlation (by
residue). You can decide how much to rebuild using
worst_percent_res_rebuild or with min_cc_res_rebuild,
or both.
min_seq_identity_percent= 50.0 The sequence in your input PDB file will be
adjusted to match the sequence in your sequence
file (if any). If there are insertions/deletions
in your model and the wizard does not seem to
identify them, you can split up your PDB file by
adding records like this: BREAK You can specify
the minimum sequence identity between your
sequence file and a segment from your input PDB
file to consider the sequences to be matched.
Default is 50.0%. You might want a higher number
to make sure that deletions in the sequence are
noticed.
min_seq_identity_percent_rebuild_in_place= 50.0 The sequence in your input
PDB file will be adjusted to
match the sequence in your
sequence file (if any) You can
specify the minimum sequence
identity between your sequence
file and a segment from your
input PDB file to consider the
sequences to be matched. Default
is 50.0%. You might want a
higher number to make sure that
deletions in the sequence are
noticed. The value you specify
applies to rebuild_in_place
only. Use
min_seq_identity_percent instead
for non rebuild_in_place runs.
model_list= None This keyword lets you name any number of PDB files to
consider as starting models for model-building. NOTE: This
differs from consider_main_chain_list which will try to add
your PDB files EVERY cycle of merging models. In contrast
model_list will only do it on the first cycle. NOTE: this only
uses the main-chain atoms of your PDB files.
modify_outside_delta_solvent= 0.05 You can set the initial solvent content
to be a little lower than calculated when you
are running modify_outside_model Usually 0.05
is fine.
modify_outside_model= Yes *No True False You can choose whether to modify
the density in the "protein" region outside the
region specified in your current model by matching
histograms with the region that is specified by that
model. This can help by raising the density in this
protein region up to a value similar to that where
atoms are already placed.
multiple_models= Yes *No True False You can build a set of models, all
compatible with your data. You can specify how many models
with multiple_models_number. If you are using
rebuild_in_place you can specify whether to generate
starting models or not with multiple_models_starting.
multiple_models_first= 1 Specify which model to build first
multiple_models_group_number= 5 You can build several initial models and
merge them. Normally 5 initial models is
fine.
multiple_models_last= 20 Specify which model to end with
multiple_models_number= 20 Specify how many models to build.
multiple_models_starting= *Yes No True False You can specify how to
generate starting models for multiple models. If
you are using rebuild_in_place and you specify
"Yes" then the Wizard will rebuild your starting
model at the resolution specified in
multiple_models_starting_resolution. If you are
not using rebuild_in_place the Wizard will always
build a starting model at the current resolution.
multiple_models_starting_resolution= 4.0 You can set the resolution for
rebuilding an initial model. A value
of 0.0 will use the resolution of the
dataset.
n_box_target= None You can tell the Wizard how many omit boxes to try and
set up (but it will not necessarily choose your number
because it has to be nicely divisible into boxes that fit
your asymmetric unit). A suitable number is 24. The larger
the number of boxes, the better the map will be, but the
longer it will take to calculate the map.
n_cycle_build= -1 Choose number of cycles (3). This does not apply if
TEXTAL is selected for build_type
n_cycle_build_max= 6 Maximum number of cycles for iterative model-building,
starting from experimental phases without a model. Even
if a satisfactory model is not found, a maximum of
n_cycle_build_max cycles will be carried out.
n_cycle_build_min= 1 Minimum number of cycles for iterative model-building,
starting from experimental phases without a model. Even
if a satisfactory model is found, n_cycle_build_min
cycles will be carried out.
n_cycle_image_min= 3 Pattern recognition (resolve_pattern) and fragment
identification ("image based density modification") are
used as part of the density modification process. These
are normally only useful in the first few cycles of
iterative model-building. This script tries
model-building both with and without including image
information, and proceeds with the most complete model.
Once at least n_cycle_image_min cycles have been carried
out with image information, if the image-based map
results in a less-complete model than the one without
image information, image information is no longer
included.
n_cycle_rebuild_in_place= None Number of cycles for rebuild_in_place for
multiple models only
n_cycle_rebuild_max= 10 Maximum number of cycles for iterative
model-rebuilding, starting from a model. Even if a
satisfactory model is not found, a maximum of
n_cycle_rebuild_max cycles will be carried out.
n_cycle_rebuild_min= 1 Mininum number of cycles for iterative
model-rebuilding, starting from a model. Even if a
satisfactory model is found, n_cycle_rebuild_min
cycles will be carried out.
n_cycle_rebuild_omit= 10 Model-building is normally carried out using the
"best" available map. If omit_on_rebuild is Yes, then
every n_cycle_rebuild_omit cycle of model rebuilding,
a composite omit map is used instead. If you specify
0 and omit_on_rebuild is Yes, omit maps will be used
every cycle. Normally every 10th cycle is optimal.
n_mini= 10 You can choose how many times to retrace your model in
"retrace_before_build"
n_random_frag= 0 In resolve building you can randomize each fragment
slightly so as to generate more possibilities for tracing
based on extending it.
n_random_loop= 3 Number of randomized tries from each end for building
loops If 0, then one try. If N, then N additional tries with
randomization based on rms_random_loop.
n_rebuild_in_place= 1 You can choose how many times to rebuild your model
in place with rebuild_in_place
n_try_rebuild= 2 Number of attempts to build each segment of chain
n_xyz_list= None You can specify the grid to use for map calculations.
nbatch= 3 You can specify the number of processors to use (nproc) and the
number of batches to divide the data into for parallel jobs.
Normally you will set nproc to the number of processors available
and leave nbatch alone. If you leave nbatch as None it will be set
automatically, with a value depending on the Wizard. This is
recommended. The value of nbatch can affect the results that you
get, as the jobs are not split into exact replicates, but are
rather run with different random numbers. If you want to get the
same results, keep the same value of nbatch.
ncs_copies= None Number of copies of the molecule in the au (note: only one
type of molecule allowed at present)
ncs_refine_coord_sigma_from_rmsd= Yes *No True False You can choose to use
the current NCS rmsd as the value of the
sigma for NCS restraints. See also
ncs_refine_coord_sigma_from_rmsd_ratio
ncs_refine_coord_sigma_from_rmsd_ratio= 1.0 You can choose to multiply the
current NCS rmsd by this value
before using it as the sigma for
NCS restraints See also
ncs_refine_coord_sigma_from_rmsd
ncycle_refine= 3 Choose number of refinement cycles (3)
no_merge_ncs_copies= Yes *No True False Normally False (do merge NCS
copies). If True, then do not use each NCS copy to try
to build the others.
nproc= 1 You can specify the number of processors to use (nproc) and the
number of batches to divide the data into for parallel jobs.
Normally you will set nproc to the number of processors available
and leave nbatch alone. If you leave nbatch as None it will be set
automatically, with a value depending on the Wizard. This is
recommended. The value of nbatch can affect the results that you
get, as the jobs are not split into exact replicates, but are rather
run with different random numbers. If you want to get the same
results, keep the same value of nbatch.
number_of_models= -1 This parameter lets you choose how many initial models
to build with RESOLVE within a single build cycle. This
parameter is now superseded by number_of_parallel_models,
which sets the number of models (but now entire build
cycles) to carry out in parallel. A zero means set it
automatically. That is what you normally should use. The
number_of_models is by default set to 1 and
number_of_parallel_models is set to the value of nbatch
(typically 4).
number_of_parallel_models= 0 This parameter lets you choose how many models
to build in parallel. A zero means set it
automatically. That is what you normally should
use. This parameter supersedes the old parameter
number_of_models. The value of number_of_models
is by default set to 1 and
number_of_parallel_models is set to the value of
nbatch (typically 4).
offset_boundary= 1.0 Specify the boundary around omit_box_pdb for
definition of omit region.
offset_boundary_background_map= None You can set the offset of the
boundary_background_map.
offsets_list= 53 7 23 You can specify an offset for the orientation of the
helix and strand templates in building. This is used in
generating different starting models.
ok_molp_score= None You can choose to include the clash score from
MolProbity as one of the scoring criteria in comparing and
merging models. The score is combined with the model-map
correlation CC by summing in a weighted clashscore. If
clashscore for a residue has a value < ok_molp_score (the
threshold defined by ok_molp_score) then its value is
(clashscore-ok_molp_score)*scale_molp_score, otherwise its
value is zero.
omit_box_end= 0 To only carry out omit in some of the omit boxes, use
omit_box_start and omit_box_end
omit_box_pdb_list= None This keyword applies if you have set OMIT region
specification to "omit_around_pdb". To automatically set
an OMIT region specify a PDB file(s) with
omit_box_pdb_list. The omit region boundaries will be
the limits in x y z of the atoms in this file, plus a
border of offset_boundary. To use only some of the atoms
in the file, specify values for starting, ending and
chain to omit (omit_res_start_list and omit_res_end_list
and omit_chain_list) If you specify more than one file
(or if you specify more than one segment of a file with
omit_chain_list or omit_res_start_list and
omit_res_end_list) then a set of omit runs will be
carried out and combined into one composite omit.
omit_box_start= 0 To only carry out omit in some of the omit boxes, use
omit_box_start and omit_box_end
omit_chain_list= None You can choose to omit just a portion of your model
keywords omit_res_start_list 3 omit_res_end_list 4
omit_chain_list chain1 (use "" to select all chains) The
residues from 3 to 4 of chain1 will be omitted. You can
specify more than one region by using the Parameter Group
Options button to add lines. If you specify more than one
region, a separate omit run will be carried out for each
one and then the maps will be put together afterwards. If
there are more than one chains in the input PDB file then
only the chain defined by omit_chain will be omitted NOTE:
Zero for start and end and "" for chain is the same as
choosing everything
omit_offset_list= 0 0 0 0 0 0 To carry out one iterative build omit, with a
region defined in grid units, enter
nxs,nxe,nys,nye,nzs,nze in omit_offset_list.
omit_on_rebuild= Yes *No True False You can specify whether to use an omit
map for building the model on rebuild cycles. Default is
Yes if you start with a model, No if you are building a
model from scratch. The omit map is calculated every
n_cycle_rebuild_omit cycles
omit_region_specification= *composite_omit omit_around_pdb You can specify
what region an omit
(simple/sa-omit/iterative-build-omit) map is to
be calculated for. Composite omit will create a
map over the entire asymmetric unit by dividing
the asymmetric unit into overlapping boxes,
calculating omit maps for each, and splicing all
the results together into a single composite
omit map. You can tell the Wizard how many omit
boxes to try and set up with the keyword
"n_box_target" (but it will not necessarily
choose your number because it has to be nicely
divisible into boxes that fit your asymmetric
unit). Omit around PDB will omit around the
region defined by the PDB file(s) you enter for
omit_box_pdb (or around the residues in that PDB
file that you specify). If you specify
omit_around_pdb then you must enter a pdb file
to omit around.
omit_res_end_list= None You can choose to omit just a portion of your model
keywords omit_res_start_list 3 omit_res_end_list 4
omit_chain_list chain1 (use " " for blank) The residues
from 3 to 4 of chain1 will be omitted. You can specify
more than one region by using the Parameter Group
Options button to add lines. If you specify more than
one region, a separate omit run will be carried out for
each one and then the maps will be put together
afterwards. If there are more than one chains in the
input PDB file then only the chain defined by omit_chain
will be omitted NOTE: Zero for start and end and "" for
chain is the same as choosing everything
omit_res_start_list= None | |||||||||||||||||||||||||