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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 a parameters file. 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, 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 parameters files. All three versions are identical except in the way that they take commands from the user. See Using the PHENIX Wizards 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 parameters files. 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 by default carried out if the starting model differs less than about 50% in sequence from the desired model, and otherwise procedure (b) is used. It is generally a good idea to specify which you want to happen using the keyword "rebuild_in_place=True" (to keep the basic input model) or "rebuild_in_place=False" (to build a new model). What the AutoBuild wizard needs to run
...and optional files
Anisotropy correction and B-factor sharpeningThe AutoBuild wizard will apply an anistropy correction and B-factor sharpening to all the raw experimental data by default (controlled by they keyword remove_aniso=True). The target overall Wilson B factor can be set with the keyword b_iso, as in b_iso=25. By default the target Wilson B will be 10 times the resolution of the data (e.g., if the resolution is 3 A then b_iso=30.), or the actual Wilson B of the data, whichever is lower. If an anisotropy correction is applied then the entire AutoBuild run will be carried out with anisotropy-corrected and sharpened data. At the very end of the run the final model will be re-refined against the uncorrected refinement data and this re-refined model and the uncorrected refinement data (with freeR flags) will be written out as overall_best.pdb and overall_best_refine_data.mtz. 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 Using the PHENIX Wizards for how to do this. Some of the most common parameters are: data=w1.sca # data file
model=coords.pdb # starting model
rebuild_in_place=true # rebuild input model in place
rebuild_in_place=false # build a new model; add or subtract residues
# from input model as necessary
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)
Running from a parameters fileYou can run phenix.autobuild from a parameters file. This is often convenient because you can generate a default one with: phenix.autobuild --show_defaults > my_autobuild.effand then you can just edit this file to match your needs and run it with: phenix.autobuild my_autobuild.eff 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. Twinning and AutoBuildAutoBuild does not know about twinning, but you can incorporate a twin law into the refinement steps in the AutoBuild procedure if your crystal is twinned. Use phenix.xtriage to identify twinning and the twin law. Then specify the twin law in a parameters file (see next section) and provide that to AutoBuild with the keyword such as "refine_eff_file=twin_law.eff" You may also want to try using the keyword "two_fofc_in_rebuild" which will use the 2Fo-Fc map from phenix.refine in model-building. 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 parameters file. 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 resultsThe key output files that are produced are:
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. NOTE: If you are using rebuild_in_place then your model must be quite similar to your sequence file, and in particular the model must not extend in the N-terminal direction beyond your sequence file. Minor edits (amino acid replacements) will be done automatically. 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:
Phenix.autobuild is set up so that you can specify the number of processors (nproc). Here is how to choose how to set it:
run_command ="command you use to submit a job to your system" background=False # probably false if this is a cluster, true if this is a multiprocessor machineIf you have a queueing system with 20 nodes, then you probably submit jobs with something like "qsub -someflags myjob.sh" # where someflags are whatever flags you use (or just "qsub myjob.sh" if no flags) Then you might use run_command="qsub -someflags" background=False nproc=20or run_command="qsub" background=False nproc=20or If you have a 20-processor machine instead, then you might say run_command=sh background=True nproc=20so that it would run your jobs with sh on your machine, and run them all in the background (i.e., all at one time). 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 via the command-line. The PHENIX-Coot interface is accessible via the command-line. When a model has been produced by the AutoSol Wizard, you can open a new window and type: phenix.autobuild cootwhich will start Coot with your current map and model. 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: Sample AutoBuild CommandsNOTE: Output files will be in subdirectories labelled "AutoBuild_run_1_" "AutoBuild_run_2_" etc. Run AutoBuild beginning with experimental dataphenix.autobuild data=solve_1.mtz seq_file=seq.dat input_ncs_file=ha.pdb Here the data in solve_1.mtz (FP SIGFP PHIB FOM HLA HLB HLC HLD) will be used as the starting point for density modification. Then a model will be built and refined. In subsequent cycles the models that have been built will be used to improve the phases in density modification. If NCS can be found from the sites in ha.pdb or from any models that are built, then NCS will be used in density modification. Run AutoBuild beginning with a model and rebuild in placephenix.autobuild data=w1.sca seq.dat model=coords.pdb \ rebuild_in_place=True Here "rebuild_in_place=True" tells AutoBuild to keep the overall model you have supplied, not to add or subtract residues from it, except that AutoBuild will try to edit the model to match the sequence in your sequence file. The AutoBuild Wizard will use your model and the data in w1.sca to generate starting phases, then it will carry out density modification to improve those phases, and adjust your model, rebuilding the model to match the resulting map and refining the model. This will be done iteratively, with the new model from each cycle being used at the start of the next one. If NCS is found in your model then it will be used in the density modification process. Add more residues to a model or rebuild a modelphenix.autobuild data=solve_1.mtz seq_file=seq.dat \ model=coords.pdb rebuild_in_place=False Here "rebuild_in_place=False" tells AutoBuild to build a new model, adding or subtracting residues as necessary. The data in solve_1.mtz (FP SIGFP PHIB FOM HLA HLB HLC HLD) will be used along with your model as the starting point for density modification. Then a new model will be built and refined. In subsequent cycles the models that have been built will be used to improve the phases in density modification. If NCS is found in your model or any model that is built, then it will be used in density modification. Run AutoBuild automatically after AutoSolphenix.autobuild after_autosolAutoBuild will identify the AutoSol run (in your working directory) with the highest overall score, then it will take the experimental phases (solve_xx.mtz or phaser_xx.mtz, where xx is the solution number) from that run, along with the corresponding density-modified map (resolve_xx.mtz) and the heavy_atom file (ha_xx.pdb_formatted.pdb) as inputs. Additionally, data for refinement are read in from exptl_fobs_freeR_flags_xx.mtz. AutoBuild will then build a model, refine it, use the refined model in density modification, then iterate the model-building, refinement, and density modification process until no further improvement in the model occurs. Merge in hires dataphenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.datThe high-resolution data in w1.sca will be used for FP and SIGFP. Other information from solve_2.mtz (PHIB FOM HLA HLB HLC HLD) will be kept. Truncate density at heavy-atom sitesphenix.autobuild data=solve_2.mtz seq_file=seq.dat input_ha_file=ha.pdb truncate_ha_sites_in_resolve=TrueThe heavy-atom sites in ha.pdb will be used to mark locations where high density is to be ignored during initial cycles of density modification. This can be useful if the heavy-atom peaks are very pronounced in the experimental map. Skip NCS in model_building and refinementphenix.autobuild data=solve_2.mtz seq_file=seq.dat find_ncs=False refine_with_ncs=FalseThe keyword "find_ncs=False" disables the finding of NCS from the models that are built and its use in density modification and model-building. The keyword "refine_with_ncs=False" disables finding NCS and its use in the refinement process. Together they prevent all use of NCS. 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. 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/ . Make a SA composite omit mapphenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=sa_omitCoefficients for the output simulated-annealing composite omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . Combine composite OMIT files from a set of parallel runs on different computersIf you run a composite OMIT job but it fails at the last step of combining files, or if you run all the individual omit boxes on different machines, you can still combine them all into one single composite omit map. You can do this by copying all the individual mtz files with map coefficients for omit regions to a single directory. Here is a script you can edit and use to combine omit maps representing different omit regions into one. NOTE: you need to ensure that the OMIT regions are defined the same in the runs where you got your overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 etc files and this run. You ensure that with the n_xyz command that sets the grid. You can copy this from one of your resolve log files created when you ran your omit (i.e., AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0/resolve.log will have a line like "nu nv nw: 32 32 32 " and you copy those numbers). ------------------------------------ #!/bin/csh -f # COMBINE OMIT SCRIPT phenix.resolve << EOD hklin exptl_fobs_phases_freeR_flags.mtz labin FP=FP SIGFP=SIGFP n_xyz 32 32 32 # YOU MUST SET THIS BASED ON THE nu nv nw in a resolve log file. solvent_content 0.85 no_build ha_file NONE combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_13 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_14 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_15 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_16 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_17 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_18 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_19 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_20 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_21 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_22 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_23 combine_map overall_best_denmod_map_coeffs.mtz_OMIT_REGION_24 omit EOD # END OF COMBINE OMIT SCRIPT 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. 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. 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 subdirectory MULTIPLE_MODELS in the file 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 setting 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. Remove the worst-fitting residues from a modelphenix.autobuild data=data.mtz model=coords.pdb \ delete_bad_residues_only=True \ input_map_file=map_coeffs.mtz \ worst_percent_res_rebuild=2 min_cc_res_rebuild=0.8The trimmed model will be in the file (the run number may vary): AutoBuild_run_1_/starting_model_trimmed.pdband the removed residues will be in the file: AutoBuild_run_1_/starting_model_removed_residues.pdbYou can delete just the worst parts of your model by setting delete_bad_residues_only=True. You can decide what parts to remove based on a minimum model-map correlation (by residue). You can decide how much to remove using worst_percent_res_rebuild or with min_cc_res_rebuild, or both. (these are the same parameters used to decide which residues to rebuild in touch_up=True). Here the input_map_file is optional; if you do not provide it then a model- based density modified map will be used to evaluate your model. 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 final models will be in the subdirectory MULTIPLE_MODELS in the file 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. Combining files from a nearly-complete autobuild run with rebuild-in-place=trueIf you have run autobuild with rebuild_in_place=True then the last step is combining the models that have been produced. If you ran the job in separate batches and want to combine the final models, you can use the script below. Note that all the models must have exactly the same set of atoms (aside from any solvent). Basically you run a dummy autobuild run to create a directory and database entries, then you copy your files there, then you run autobuild and tell it to carry on and do the combine step. -------------------------------------------------------- #!/bin/csh -f #COMBINE_MODELS SCRIPT if (-d PDS || -d AutoBuild_run_1_) then echo "Please run in a directory without PDS or AutoBuild_run_1_" exit 1 endif echo "Setting up combine models with a dummy run. NOTE: multiple_models_group_number must be correct" phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat combine_only=true multiple_models_group_number=2 multiple_models_number=1 > dummy_autobuild.log echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS" mkdir AutoBuild_run_1_/MULTIPLE_MODELS cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1 cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2 cp map_coeffs_1.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1 cp map_coeffs_2.mtz AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2 ls AutoBuild_run_1_/MULTIPLE_MODELS/ echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS" phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 > autobuild_combine.log # END OF COMBINE_MODELS SCRIPT ------------------------------------------------------- Morph an MR model and rebuild itphenix.autobuild data=data.mtz model=MR.pdb \ morph=True rebuild_in_place=False seq_file=seq.datYou can have autobuild morph your input model, distorting it to match the density-modified map that is produced from your model and data. This can be used to make an improved starting model in cases where the MR model is very different than the structure that is to be solved. For the morphing to work, the two structures must be topologically similar and differ mostly by movements of domains or motifs such as a group of helices or a sheet. The morphing process consists of identifying a coordinate shift to apply to each N (or P for nucleic acids) atom that maximizes the local density correlation between the model and the map. This is smoothed and applied to the structure to generate a morphed structure. 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 Density-modify with or without a model and make mapsYou can use the AutoBuild Wizard as a convenient way to run resolve density modification with or without including model-based information. Just use a command like this: phenix.autobuild data=data.mtz model=coords.pdb \ maps_only=True seq_file=seq.dator phenix.autobuild data=data.mtz \ maps_only=True seq_file=seq.datThe Wizard will calculate the same map that it would normally calculate given these data, and then it will write the map out and stop. Density-modify starting with your map coefficients and make mapsYou can use the AutoBuild Wizard as a convenient way to run resolve density modification starting with map coefficients you define. Just use a command like this: phenix.autobuild data=data.mtz \
maps_only=True seq_file=seq.dat \
map_file=starting_map.mtz map_labels="2FOFCWT PH2FOFCWT"
The Wizard will start with the phases in starting_map.mtz calculate the same map that it would normally calculate given
these data, and then it will write the map out and stop.
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
data= None Datafile. 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'. 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). NOTE: If you supply HL coefficients they
will be used in phase recombination. If you supply PHIB or PHIB and
FOM and not HL coefficients, then HL coefficients will be derived
from your PHIB and FOM and used in phase recombination. 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.
model= None PDB file with starting model. 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.
seq_file= Auto Sequence file. The format is plain text, with chains
separated by a line starting with > or a blank line. Any blanks
and unrecognized characters are ignored. You need only input 1
copy of each unique chain. 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" If you have a duplex DNA, enter each strand
as a separate chain.
map_file= Auto MTZ file containing starting map. 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'. This map will be used in the first cycle of
model-building. NOTE 1: If use_map_file_as_hklstart=True then
this file will be used instead to start density modification.
NOTE 2: 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"
refinement_file= Auto File for refinement. 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'. 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"
hires_file= Auto File with high-resolution data. 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'.
crystal_info
unit_cell= None Enter cell parameter (a b c alpha beta gamma)
space_group= None Space Group symbol (i.e., C2221 or C 2 2 21)
solvent_fraction= None Solvent fraction in crystals (0 to 1). This is
normally set automatically from the number of NCS
copies and the sequence.
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.
resolution= 0 High-resolution limit. Used as resolution limit for
density modification and as general default high-resolution
limit. If resolution_build or refinement_resolution are set
then they override this for model-building or refinement. If
overall_resolution is set then data beyond that resolution
is ignored completely. Zero means keep everything.
dmax= 500 Low-resolution limit
overall_resolution= 0 If overall_resolution is set, then all data beyond
this is ignored. NOTE: this is only suggested if you
have a very big cell and need to truncate the data
to allow the wizard to run at all. Normally you
should use 'resolution' and 'resolution_build' and
'refinement_resolution' to set the high-resolution
limit
sequence= None Plain text containing 1-letter code of protein sequence
Same as seq_file except the sequence is read directly, not
from a file. If both are given, seq_file is ignored.
input_files
input_labels= None Labels for input data columns
input_hires_labels= None Labels for input hires file (FP SIGFP
FreeR_flag)
input_map_labels= None Labels for input map coefficient columns (FP PHIB
FOM) NOTE: FOM is optional (set to None if you wish)
input_refinement_labels= None Labels for input refinement file columns
(FP SIGFP FreeR_flag)
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.
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
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).
keep_input_ligands= True 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= 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=True and keep_pdb_atoms=True 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= True If true, 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. If false, keep instead the ligand
coordinates.
refine_eff_file_list= None You can enter any number of refinement
parameter files. These are normally used to tell
phenix.refine defaults to apply, as well as
creating specialized definitions such as unusual
amino acid residues and linkages. These parameters
override the normal phenix.refine defaults. They
themselves can be overridden by parameters set by
the Wizard and by you, controlling the Wizard.
NOTE: Any parameters set by AutoBuild directly
(such as number_of_macro_cycles, high_resolution,
etc...) will not be taken from this parameters
file. This is useful only for adding extra
parameters not normally set by AutoBuild.
map_file_is_density_modified= False You can specify that the
input_map_file has been density modified.
(This changes the assumptions on
statistics of the map.)
map_file_fom= None You can specify the FOM of the input map file (useful
in cases where the map file has only FWT PHFWT and no FOM
column). This FOM is used to set the default smoothing
radius for the density modification solvent boundary.
use_map_file_as_hklstart= False You can specify that the file named as
input_map_file will be used as starting
coefficients for density modification in the
first cycle. NOTE: if maps_only=True and
input_map_file is set, then
use_map_file_as_hklstart will be set to True
use_map_in_resolve_with_model= False You can specify that the current
map file be used as hklstart in density
modification with a model.
aniso
remove_aniso= True Remove anisotropy from data files before use Note:
map files are assumed to be already corrected and are not
affected by this. Also the input refinement file is not
affected by this.
b_iso= None Target overall B value for anisotropy correction. Ignored if
remove_aniso = False. If None, default is minimum of (max_b_iso,
lowest B of datasets, target_b_ratio*resolution)
max_b_iso= 40. Default maximum overall B value for anisotropy
correction. Ignored if remove_aniso = False. Ignored if b_iso
is set. If used, default is minimum of (max_b_iso, lowest B
of datasets, target_b_ratio*resolution)
target_b_ratio= 10. Default ratio of target B value to resolution for
anisotropy correction. Ignored if remove_aniso = False.
Ignored if b_iso is set. If used, default is minimum of
(max_b_iso, lowest B of datasets,
target_b_ratio*resolution)
decision_making
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
r_switch= 0.4 R-value criteria for deciding whether to use R-value or
map correlation as a criteria for model quality. A good value
is 0.40
semi_acceptable_r= 0.3 Used to decide whether the model is acceptable
enough to skip rebuilding the model from scratch and
focus on adding loops and extending it. A good value
is 0.3
min_cc_res_rebuild= 0.5 You can rebuild just the worst parts of your
model by setting 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 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.
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
loop_cc_min= 0.4 You can specify the minimum correlation of density from
a loop with the map.
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.
include_molprobity= 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.
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.
scale_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 then its value is
(clashscore-ok_molp_score)*scale_molp_score, otherwise
its value is zero.
density_modification
thorough_denmod= *Auto True False Choose whether you want to go for
thorough density modification when no model is used
("False" speeds it up and for a terrible map
is sometimes better)
hl= False You can choose whether to calculate hl coeffs when doing
density modification (True) or not to do so (False). Default is No.
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.
mask_from_pdb= None You can specify a PDB file to define a mask for the
macromolecule in density modification (i.e., the solvent
boundary). All points within rad_mask_from_pdb of an atom
in the PDB file defined by mask_from_pdb will be
considered to be within the macromolecule
rad_mask_from_pdb= 2 You can define the radius for calculation of the
protein mask Applies only to mask_from_pdb
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= 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.
truncate_ha_sites_in_resolve= *Auto True False You can choose to
truncate the density near heavy-atom sites
at a maximum of 2.5 sigma. This is useful
in cases where the heavy-atom sites are
very strong, and rarely hurts in cases
where they are not. The heavy-atom sites
are specified with
"input_ha_file" and the radius
is rad_mask
rad_mask= None You can define the radius for calculation of the protein
mask Applies only to truncate_ha_sites_in_resolve. Default is
resolution of data.
use_resolve_fragments= True This script normally uses information from
fragment identification as part of density
modification for the first few cycles of
model-building. Fragments are identified during
model-building. The fragments are used, with
weighting according to the confidence in their
placement, in density modification as targets for
density values.
use_resolve_pattern= True Local pattern identification is normally used
as part of density modification during the first
few cycles of model building.
use_hl_anom_in_denmod= False Default is False (use HL coefficients in
density modification) NOTE: if True, you must
supply HLanom coefficients Allows you to specify
that HL coefficients including only the phase
information from the imaginary (anomalous
difference) contribution from the anomalous
scatterers are to be used in density
modification. Two sets of HL coefficients are
produced by Phaser. HLA HLB etc are HL
coefficients including the contribution of both
the real scattering and the anomalous
differences. HLanomA HLanomB etc are HL
coefficients including the contribution of the
anomalous differences alone. These HL
coefficients for anomalous differences alone are
the ones that you will want to use in cases where
you are bringing in model information that
includes the real scattering from the model used
in Phaser, such as when you are carrying out
density modification with a model or refinement
of a model If use_hl_anom_in_denmod=True then the
HLanom HL coefficients from Phaser are used in
density modification
use_hl_anom_in_denmod_with_model= False See use_hl_anom_in_denmod If
use_hl_anom_in_denmod=True then the
HLanom HL coefficients from Phaser are
used in density modification with a
model
mask_as_mtz= False Defines how omit_output_mask_file
ncs_output_mask_file and protein_output_mask_file are
written out. If mask_as_mtz=False it will be a ccp4 map. If
mask_as_mtz=True it will be an mtz file with map
coefficients FP PHIM FOMM (all three required)
protein_output_mask_file= None Name of map to be written out
representing your protein (non-solvent)
region. If mask_as_mtz=False the map will be a
ccp4 map. If mask_as_mtz=True it will be an
mtz file with map coefficients FP PHIM FOMM
(all three required)
ncs_output_mask_file= None Name of map to be written out representing
your ncs asymmetric unit. If mask_as_mtz=False the
map will be a ccp4 map. If mask_as_mtz=True it
will be an mtz file with map coefficients FP PHIM
FOMM (all three required)
omit_output_mask_file= None Name of map to be written out representing
your omit region. If mask_as_mtz=False the map
will be a ccp4 map. If mask_as_mtz=True it will
be an mtz file with map coefficients FP PHIM FOMM
(all three required)
maps
maps_only= 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.
n_xyz_list= None You can specify the grid to use for map calculations.
model_building
build_type= *RESOLVE RESOLVE_AND_BUCCANEER You can choose to build
models with RESOLVE or with RESOLVE and BUCCANEER #and
TEXTAL 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. For BUCCANEER model building you
need CCP4 version 6.1.2 or higher and BUCCANEER version
1.3.0 or higher
allow_negative_residues= 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.
highest_resno= None Highest residue number to be considered
"placed" in sequence for rebuild_in_place
semet= False You can specify that the dataset that is used for
refinement is a selenomethionine dataset, and that the model
should be the SeMet version of the protein, with all SD of MET
replaced with Se of MSE.
use_met_in_align= *Auto True False You can use the heavy-atom positions
in input_ha_file as markers for Met SD positions.
base_model= None You can enter a PDB file with coordinates to be used as
a starting point for model-building. These coordinates will
be included in the same way as fragments placed by searching
for helices and strand in initial model-building. Note the
difference from the use of models in
consider_main_chain_list, which are merged with models after
they are built. NOTE: Only use this if you want to keep the
input model and just add to it.
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.
dist_connect_max_helices= None Set maximum distance between ends of
helices and other ends to try and connect them
in insert_helices.
edit_pdb= True 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
helices_strands_only= 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 'False' as standard building is
quick. When your structure is solved by AutoSol,
go on to AutoBuild and build a more complete model
(still using helices_strands_only=False). NOTE:
helices_strands_only does not apply in AutoSol if
phase_improve_and_build=True
helices_strands_start= False You can choose to use a quick
model-building method that builds secondary
structure as a way to get started...then model
completion is done as usual. (Contrast with
helices_strands_only which only does secondary
structure)
cc_helix_min= None Minimum CC of helical density to map at low
resolution when using helices_strands_only
cc_strand_min= None Minimum CC of strand density to map when using
helices_strands_only
trace_loops= False Use trace_loops algorithm in loop fitting
standard_loops= True Use standard_loops algorithm in loop fitting
loop_lib= False Use loop_lib algorithm in loop fitting
include_input_model= True 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. It also defines whether the
input model is to be included in combination steps
during initial model-building. 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.
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.
merge_models= False You can choose to only merge any input models and
write out the resulting model. The best parts of each
model will be kept based on model-map correlation.
Normally used along with number_of_parallel_models=1
morph= False You can choose whether to distort your input model in order
to match the current working map. This may be useful for MR
models that are quite distant from the correct structure.
morph_cycles= 2 Number of iterations of morphing each time it is run.
morph_rad= 7 Smoothing radius for morphing. The density from your model
and from the map are calculated with the radius rad_morph,
then they are adjusted to overlap optimally
n_ca_enough_helices= None Set maximum number of CA to add to ends of
helices and other ends to try and connect them in
insert_helices.
delta_phi= 20 Approximate angular sampling for search for regular
secondary structure in building
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.
ps_in_rebuild= False You can choose to use a prime-and-switch resolve
map in all cycles of rebuilding instead of a
density-modified map. This is normally used in
combination with maps_only to generate a prime-and-switch
map.
use_ncs_in_ps= False You can choose to use NCS in prime-and-switch
remove_outlier_segments_z_cut= 3.0 You can remove any segments that are
not assigned to sequence during
model-building if the mean density at
atomic positions are more than
remove_outlier_segments_z_cut sd lower
than the mean for the structure.
refine= True This script normally refines the model during building. Say
False to skip refinement
reference_model= None You can specify a reference model for refinement
resolution_build= 0 Enter the high-resolution limit for model-building.
If 0.0, the value of resolution is used as a default.
restart_cycle_after_morph= 5 Morphing (if morph=True) will go only up to
this cycle, and then the morphed PDB file
will be used as a starting PDB file from then
on, removing all previous models. If
restart_cycle_after_morph=0 then the model
will be morphed and not rebuilt
retrace_before_build= False You can choose to retrace your model n_mini
times and use a map based on these retraced models
to start off model-building. This is the default
for rebuilding models if you are not using
rebuild_in_place. You can also specify
n_iter_rebuild, the number of cycles of
retrace-density-modify-build before starting the
main build.
reuse_chain_prev_cycle= True You can choose to allow model-building to
include atoms from each cycle in the model the
next cycle or not
richardson_rotamers= *Auto True False You can choose to use the rotamer
library from SC Lovell, JM Word, JS Richardson and
DC Richardson (2000) " The Penultimate Rotamer
Library" Proteins: Structure Function and
Genetics 40 389-408. if you wish. Typically this
works well in RESOLVE model-building for
nearly-final models but not as well earlier in the
process . Default (Auto) is to use these rotamers
for rebuild_in_place but not otherwise.
rms_random_frag= None Rms random position change added to residues on
ends of fragments when extending them If you enter a
negative number, defaults will be used.
rms_random_loop= None Rms random position change added to residues on
ends of loops in tries for building loops If you enter
a negative number, defaults will be used.
start_chains_list= None You can specify the starting residue number for
each of the unique chains in your structure. If you
use a sequence file then the unique chains are
extracted and the order must match the order of your
starting residue numbers. For example, if your
sequence file has chains A and B (identical) and
chains C and D (identical to each other, but
different than A and B) then you can enter 2 numbers,
the starting residues for chains A and C. NOTE: you
need to specify an input sequence file for
start_chains_list to be applied.
trace_as_lig= False You can specify that in building steps the ends of
chains are to be extended using the LigandFit algorithm.
This is default for nucleic acid model-building.
track_libs= False You can keep track of what libraries each atom in a
built structure comes from.
two_fofc_in_rebuild= False You can choose to use a sigmaa-weighted
2Fo-Fc map in all cycles of rebuilding instead of a
density-modified map. If the model is poor this can
sometimes allow model-building in place to work
even when it will not for density-modified maps.
refine_map_coeff_labels= "2FOFCWT PH2FOFCWT" You can pick which map
coefficients from phenix.refine to use if
two_fofc_in_rebuild=True
filled_2fofc_maps= True You can choose to use filled 2Fo-Fc maps when
two_fofc_in_rebuild is used. Default is True
map_phasing= False You can choose to use statistical density
modification starting with a 2mFo-DFc map, including model
information instead of a standard density-modified map.
This density modification will include NCS if present.
use_any_side= True You can choose to have resolve model-building place
the best-fitting side chain at each position, even if the
sequence is not matched to the map.
use_cc_in_combine_extend= False You can choose to use the correlation of
density rather than density at atomic
positions to score models in combine_extend
multiple_models
combine_only= 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.
multiple_models= 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= True You can specify how to generate starting
models for multiple models. If you are using
rebuild_in_place and you specify
"True" 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 You can set the resolution for
rebuilding an initial model. A
value of 0.0 will use the
resolution of the dataset.
place_waters_in_combine= True You can choose whether phenix.refine
automatically places ordered solvent (waters)
during the last cycle of multiple-model
generation. This is separate from place_waters,
which applies to all other cycles.
ncs
find_ncs= *Auto 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 False 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.
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.
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= 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 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
no_merge_ncs_copies= False Normally False (do merge NCS copies). If
True, then do not use each NCS copy to try to build
the others.
optimize_ncs= True This script normally deduces ncs information from the
NCS in chains of models that are built during iterative
model-building. Optimize NCS adds a step to try and make
the molecule formed by NCS as compact as possible, without
losing any point-group symmetry.
use_ncs_in_build= True Use NCS information in the model assembly stage
of model-building. Also if no_merge_ncs_copies is not
set, then use each NCS copy to try to build the
others.
omit
composite_omit_type= *None simple_omit refine_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. refine_omit - as simple_omit, but
refine with standard 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.
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_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_omit= 10 Model-building is normally carried out using
the "best" available map. If
omit_on_rebuild is True, 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 True, omit maps will be
used every cycle. Normally every 10th cycle is
optimal.
offset_boundary= 2. Specify the boundary in A around atoms in
omit_box_pdb for definition of omit region. Contrast
with omit_boundary which applies for composite omit
omit_boundary= 2. Specify the boundary in A around atoms in omit_boxes
for definition of omit region. Contrast with
offset_boundary which applies for omit_box_pdb
omit_box_start= 0 To only carry out omit in some of the omit boxes, use
omit_box_start and omit_box_end
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_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
listing them separated by spaces 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= False You can specify whether to use an omit map for
building the model on rebuild cycles. Default is True
if you start with a model, False if you are building a
model from scratch. The omit map is calculated every
n_cycle_rebuild_omit cycles
omit_selection= None Selection string defining atoms in input pdb to be
used to define the OMIT region. For use with
omit_region_specification=omit_selection
omit_region_specification= *composite_omit omit_around_pdb
omit_selection 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. If
you specify omit_selection you must enter a
selection string in omit_selection
omit_res_start_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
more than one region by listing them separated by
spaces 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 rebuilt. NOTE: Zero for start and end and
"" for chain is the same as choosing
everything
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 more
than one region by listing them separated by spaces
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
rebuild_in_place
min_seq_identity_percent_rebuild_in_place= 50 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.
n_cycle_rebuild_in_place= None Number of cycles for rebuild_in_place for
multiple models only
n_rebuild_in_place= 1 You can choose how many times to rebuild your
model in place with rebuild_in_place
rebuild_chain_list= None You can choose to rebuild just a portion of
your model keywords rebuild_res_start_list 3
rebuild_res_end_list 4 rebuild_chain_list chain1
(use " " for blank). The residues from 3
to 4 of chain1 will be rebuilt. You can specify more
than one region by using the Parameter Group Options
button to add lines. If there are more than one
chains in the input PDB file then only the chain
defined by rebuild_chain will be rebuilt. The
smallest region that can be rebuilt is 4 residues.
rebuild_in_place= *Auto True False You can choose to rebuild your model
while fixing the sequence alignment by iteratively
rebuilding segments within the model. This is done
n_rebuild_in_place times, then the models are
recombined, taking the best-fitting parts of each.
Crossovers allowed where main-chain atom rmsd is less
than dist_close. Note that the sequence of the input
model must match the supplied sequence closely enough
to allow a clear alignment. Also this method does not
build any new chain, it just moves the existing model
around. Normally this procedure is useful if the model
is greater than 95% identical with the target
sequence. You can include information directly from
the starting model if you want with the keyword
include_input_model. Then this model will be
recombined with the models that are built based on it.
Note that this requires that the input model have a
sequence that is identical to the model to be rebuilt.
You can also rebuild just a portion of the model with
the keywords keywords rebuild_res_start_list 3
rebuild_res_end_list 4 rebuild_chain_list chain1 (use
" " for blank) The residues from 3 to 4 of
chain1 will be rebuilt. You can specify more than one
region by using the Parameter Group Options button to
add lines NOTE: if a region cannot be rebuilt the
original coordinates will be preserved for that
region.
rebuild_near_chain= None You can specify where to rebuild either with
rebuild_res_start_list rebuild_res_end_list
rebuild_chain_list or with rebuild_near_res and
rebuild_near_chain and rebuild_near_dist.
rebuild_near_dist= 7.5 You can specify where to rebuild either with
rebuild_res_start_list rebuild_res_end_list
rebuild_chain_list or with rebuild_near_res and
rebuild_near_chain and rebuild_near_dist.
rebuild_near_res= None You can specify where to rebuild either with
rebuild_res_start_list rebuild_res_end_list
rebuild_chain_list or with rebuild_near_res and
rebuild_near_chain and rebuild_near_dist.
rebuild_res_end_list= None You can choose to rebuild just a portion of
your model keywords rebuild_res_start_list 3
rebuild_res_end_list 4 rebuild_chain_list chain1
(use " " for blank). The residues from 3
to 4 of chain1 will be rebuilt. You can specify
more than one region by using the Parameter Group
Options button to add lines. If there are more
than one chains in the input PDB file then only
the chain defined by rebuild_chain will be
rebuilt. The smallest region that can be rebuilt
is 4 residues.
rebuild_res_start_list= None You can choose to rebuild just a portion of
your model keywords rebuild_res_start_list 3
rebuild_res_end_list 4 rebuild_chain_list chain1
(use " " for blank). The residues from
3 to 4 of chain1 will be rebuilt. You can
specify more than one region by using the
Parameter Group Options button to add lines. If
there are more than one chains in the input PDB
file then only the chain defined by
rebuild_chain will be rebuilt. The smallest
region that can be rebuilt is 4 residues.
rebuild_side_chains= False You can choose to replace side chains (with
extend_only) before rebuilding the model (not
normally used)
redo_side_chains= True You can chooses to have AutoBuild choose whether
to replace all your side chains in rebuild_in_place,
taking new ones if they fit the density better. If
True, this is applied to all side chains, not only
those that are rebuilt.
replace_existing= True In rebuild_in_place the usual default is to force
the replacement of all residues, even if the rebuilt
ones are not as good a fit as the original. The
rebuilt model is then crossed with the original model
(if include_input_model=True) and the better parts of
each are then kept. You can override the replacement
of all residues in the initial model-building by
saying "False" (do not force replacement of
residues, keep whatever is better). Additionally if
you set the "touch_up" flag then the default
is "True": keep whatever is better.
delete_bad_residues_only= False You can simply delete the worst parts of
your model and write out the resulting model
with delete_bad_residues_only=True The
criteria used are the ones set with touch_up.
Any residues that would be rebuild by
touch_up=True will be deleted by
delete_bad_residues_only. NOTE:
delete_bad_residues_only ignores ligands,
waters etc. so you may need to put them back
in afterwards.
touch_up= False You can rebuild just the worst parts of your model by
setting touch_up=True. You can decide what parts to rebuild
based on an minimum model-map correlation (by residue). This
is set with min_cc_residue_rebuild=0.82 Alternatively you can
rebuild the worst percentage of these:
worst_percent_res_rebuild=6. If a value is set for both of
these then residues qualifying in either way are rebuilt.
NOTE: touch_up is only available with rebuild_in_place.
touch_up_extra_residues= None Number of residues on each side of the
residues identified in touch_up that you want
to rebuild. Normally you will want to rebuild
one or more on each side.
worst_percent_res_rebuild= 2 You can rebuild just the worst parts of
your model by setting touch_up=True. You can
decide how much to rebuild using
worst_percent_res_rebuild or with
min_cc_res_rebuild, or both.
smooth_range= None You can specify what number of residues to smooth in
making choices for touch_up and delete_bad_residues_only
Typically use 3 or 5.
smooth_minimum_length= None If specified, then any segments remaining
after smoothing that are shorter than
smooth_mininum_length will be removed.
refinement
refine_b= True You can choose whether phenix.refine is to refine
individual atomic displacement parameters (B values)
refine_se_occ= True You can choose to refine the occupancy of SE atoms
in a SEMET structure (default=True). This only applies if
semet=true
skip_clash_guard= True Skip refinement check for atoms that clash
correct_special_position_tolerance= None Adjust tolerance for special
position check. If 0., then check
for clashes near special positions
is not carried out. This sometimes
allows phenix.refine to continue
even if an atom is near a special
position. If 1., then checks within
1 A of special positions. If None,
then uses phenix.refine default. (1)
use_mlhl= True This script normally uses information from the input file
(HLA HLB HLC HLD) in refinement. Say No to only refine on Fobs
place_waters= True You can choose whether phenix.refine automatically
places ordered solvent (waters) during the refinement
process.
refinement_resolution= 0 Enter the high-resolution limit for refinement
only. This high-resolution limit can be different
than the high-resolution limit for other steps.
The default ("None" or 0.0) is to use
the overall high-resolution limit for this run
(as set by resolution)
ordered_solvent_low_resolution= None You can choose what resolution
cutoff to use fo placing ordered solvent
in phenix.refine. If the resolution of
refinement is greater than this cutoff,
then no ordered solvent will be placed,
even if
refinement.main.ordered_solvent=True.
link_distance_cutoff= 3 You can specify the maximum bond distance for
linking residues in phenix.refine called from the
wizards.
r_free_flags_fraction= 0.1 Maximum fraction of reflections in the free R
set. You can choose the maximum fraction of
reflections in the free R set and the maximum
number of reflections in the free R set. The
number of reflections in the free R set will be
up the lower of the values defined by these two
parameters.
r_free_flags_max_free= 2000 Maximum number of reflections in the free R
set. You can choose the maximum fraction of
reflections in the free R set and the maximum
number of reflections in the free R set. The
number of reflections in the free R set will be
up the lower of the values defined by these two
parameters.
r_free_flags_use_lattice_symmetry= True When generating r_free_flags you
can decide whether to include lattice
symmetry (good in general, necessary
if there is twinning).
r_free_flags_lattice_symmetry_max_delta= 5 You can set the maximum
deviation of distances in the
lattice that are to be
considered the same for
purposes of generating a
lattice-symmetry-unique set of
free R flags.
allow_overlapping= False You can allow atoms in your ligand files to
overlap atoms in your protein/nucleic acid model.
This overrides 'keep_pdb_atoms' Useful in early
stages of model-building and refinement The ligand
atoms get the altloc indicator 'L' NOTE: The ligand
occupancy will be refined by default if you set
allow_overlapping=True (because of the altloc
indicator) You can turn this off with
fix_ligand_occupancy=True
fix_ligand_occupancy= None If allow_overlapping=True then ligand
occupancies are refined as a group. You can turn
this off with fix_ligand_occupancy=true NOTE: has
no effect if allow_overlapping=False
remove_outlier_segments= True You can remove any segments that are not
assigned to sequence if their mean B values are
more than remove_outlier_segments_z_cut sd
higher than the mean for the structure. NOTE:
this is done after refinement, so the R/Rfree
are no longer applicable; the remarks in the
PDB file are removed
twin_law= None You can specify a twin law for refinement like this:
twin_law='-h,k,-l'
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)
refine_before_rebuild= True You can choose to refine the input model
before rebuilding it
refine_with_ncs= True This script can allow phenix.refine to
automatically identify NCS and use it in refinement.
NOTE: ncs refinement and placing waters automatically
are mutually exclusive at present.
refine_xyz= True You can choose whether phenix.refine is to refine
coordinates
s_annealing= False You can choose to carry out simulated annealing
during the first refinement after initial model-building
skip_hexdigest= False You may wish to ignore the hexdigest of the free R
flags in your input PDB file if (1) the dataset you
provide is not identical to the one that you refined
with (but has the same free R flags), or (2) you are
providing both an input_data_file and an
input_refinement_file or input_hires_file and. In the
second case, the resulting composite file may not have
the same hexdigest even though the free R flags are
copied over. The default is to set skip_hexdigest=True
for case #2. For case #1 you have to tell the Wizard to
skip the hexdigest (because it cannot know about this).
use_hl_anom_in_refinement= False See use_hl_anom_in_denmod. If
use_hl_anom_in_refinement=True then the
HLanom HL coefficients from Phaser are used
in refinement
thoroughness
build_outside= True Define whether to use the BuildOutside module in
model_building
connect= True Define whether to use the connect module in
model_building. 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).
extensive_build= False You can choose whether to build a new model on
every cycle and carry out extra model-building steps
every cycle. Default is False (build a new model on
first cycle, after that carry out extra steps).
fit_loops= True You can fit loops automatically if sequence alignment
has been done.
insert_helices= True Define whether to use the insert_helices module in
model_building. This module tries to insert helices
identified with find_helices_strands into the current
working model. This can be useful as the standard build
sometimes builds strands into helical density at low
resolution.
n_cycle_build= None Choose number of cycles of building and chain
extension during each cycle of model-building. (default
of 1 ).
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_rebuild_max= 15 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_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_try_rebuild= 2 Number of attempts to build each segment of chain
ncycle_refine= 3 Choose number of refinement cycles (3)
number_of_models= None 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. None or 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. None or 0 means
set it automatically. That is what you
normally should use. You can set this to 1 to
prevent the wizard from running multiple jobs
in parallel
skip_combine_extend= False You can choose whether to skip the
combine-extend step in model-building if only one
model is available
fully_skip_combine_extend= False You can choose whether to skip the
combine-extend step in model-building in all
cases
thorough_loop_fit= True Try many conformations and accept them even if
the fit is not perfect? If you say True the
parameters for thorough loop fitting are:
n_random_loop=100 rms_random_loop=0.3
rho_min_main=0.5 while if you say False those for
quick loop fitting are: n_random_loop=20
rms_random_loop=0.3 rho_min_main=1.0
general
coot_name= "coot" If your version of coot is called something else, then
you can specify that here.
i_ran_seed= 72432 Random seed (positive integer) for model-building and
simulated annealing refinement
raise_sorry= False You can have any failure end with a Sorry instead of
simply printout to the screen
background= True 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='sh ' (or similar, sh is
default) then normally you will use background=True so that
all the jobs run simultaneously.
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:....
cache_resolve_libs= True Use caching of resolve libraries to speed up
resolve
resolve_size= 12 Size for solve/resolve
("","_giant",
"_huge","_extra_huge" or a number
where 12=giant 18=huge
check_run_command= False You can have the wizard check your run command
at startup
run_command= "sh " When you specify nproc=nn, you can run the
subprocesses as jobs in background with sh (default) or
submit them to a queue with the command of your choice
(i.e., qsub ). If you have a multi-processor machine, use
sh. If you have a cluster, use qsub or the equivalent
command for your system. NOTE: 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 nproc is greater than 1 and you use
run_command='sh '(or similar, sh is default) then normally
you will use background=True so that all the jobs run
simultaneously.
last_process_is_local= True If true, run the last process in a group in
background with sh as part of the job that is
submitting jobs. This prevents having the job
that is submitting jobs sit and wait for all the
others while doing nothing
skip_r_factor= False You can skip R-factor calculation if refinement is
not done and maps_only=True
skip_xtriage= False You can bypass xtriage if you want. This will
prevent you from applying anisotropy corrections, however.
base_path= None You can specify the base path for files (default is
current working directory)
temp_dir= None Define a temporary directory (it must exist)
clean_up= True At the end of the entire run the TEMP directories will be
removed if clean_up is True. The default is yes, delete these
directories. If you want to remove them after your run is
finished use a command like "phenix.autobuild run=1
clean_up=True" Files listed in keep_files will not be
deleted
solution_output_pickle_file= None At end of run, write solutions to this
file in output directory if defined
title= None Enter any text you like to help identify what you did in
this run
top_output_dir= None This is used in subprocess calls of wizards and to
tell the Wizard where to look for the STOPWIZARD file.
wizard_directory_number= None This is used by the GUI to define the run
number for Wizards. It is the same as
desired_run_number NOTE: this value can only be
specified on the command line, as the directory
number is set before parameters files are read.
verbose= False Command files and other verbose output will be printed
extra_verbose= False Facts and possible commands will be printed every
cycle if True
debug= False You can have the wizard stop with error messages about the
code if you use debug. NOTE: you cannot use Pause with debug.
Additionally the output goes to the terminal if you specify
"debug=True"
require_nonzero= True Require non-zero values in data columns to
consider reading in.
remove_path_word_list= None List of words identifying paths to remove
from PATH These can be used to shorten your PATH.
For example... cns ccp4 coot would remove all
paths containing these words except those also
containing phenix. Capitalization is ignored.
fill= False Fill in all missing reflections to resolution res_fill.
Applies to density modified maps. See also filled_2fofc_maps in
autobuild.
res_fill= None Resolution for filling in missing data (default = highest
resolution of any datafile). Only applies to density modified
maps. Default is fill to high resolution of data. Ignored if
fill=False
keep_files= overall_best* AutoBuild_run_*.log List of files that are not
to be cleaned up. wildcards permitted
after_autosol= False You can specify that you want to continue on
starting with the highest-scoring run of AutoSol in your
working directory.
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.
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. If you set
nproc=Auto and your machine has n processors, then it will use
n-1 processors, or 1 if only 1 is available
quick= False Run everything quickly (number_of_parallel_models=1
n_cycle_build_max=1 n_cycle_rebuild_max=1)
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' "
resolve_pattern_command_list= None Commands for resolve_pattern. One per
line in the form: keyword value value can
be optional Examples: 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_pattern_command_list="'resolut
ion 200 20' 'hklin test.mtz' "
ignore_errors_in_subprocess= False Try to ignore errors in sub-processes
This is useful in cases where a very rare
crash occurs and you want to just ignore
that step and go on.
send_notification= False
notify_email= None
special_keywords
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.
run_control
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.
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.
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.
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.
carry_on= None Set carry_on to True to carry on with highest-numbered
run from where you left off.
run= None Set run to n to continue with run n where you left off.
copy_run= None Set copy_run to n to copy run n to a new run and continue
where you left off.
display_runs= None List all runs for this wizard.
delete_runs= None List runs to delete: 1 2 3-5 9:12
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 or AutoBuild like this:
input_refinement_labels="FP SIGFP FreeR_flags"
# each individual label counts
dry_run= False Just read in and check parameter names
params_only= False Just read in and return parameter defaults. Not for
general use
display_all= False Just read in and display parameter defaults
non_user_parameters These are obsolete parameters and parameters that the
wizards use to communicate among themselves. Not
normally for general use.
gui_output_dir= None Used only by the GUI
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="")
extend_try_list= True 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.
force_combine_extend= False You can choose whether to force the
combine-extend step in model-building
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.
oasis_cnos= None Enter number of C N O and S atoms here if you have
OASIS and want to run it before resolve density modification
like this: "C 250 N 121 O 85 S 3"
offset_boundary_background_map= None You can set the offset of the
boundary_background_map.
sg= None Obsolete. Use space_group instead
input_data_file= None Not normally used (same as "data=").
input_map_file= Auto Not normally used. (Same as map_file).
input_refinement_file= Auto Not normally used. Same as refinement_file
input_pdb_file= None Not normally used. Same as "model="
input_seq_file= Auto Not normally used. Same as seq_file
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