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Automated molecular replacement with AutoMR
Author(s)
PurposePurpose of the AutoMR WizardThe AutoMR Wizard provides a convenient interface to Phaser molecular replacement and feeds the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding. The AutoMR Wizard begins with datafiles with structure factor amplitudes and uncertainties, a search model or models, and identifies placements of the search models that are compatible with the data. UsageThe AutoMR 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. NOTE: You may find it easiest to run the GUI version of AutoMR when you are learning how to use it, and then to move to the command-line or script versions later, as the GUI version will take you through all the necessary steps of organizing your data. Summary of inputs and outputs for AutoMRInput data file. This file can be in most any format, and must contain either amplitudes or intensities and sigmas. You can specify what resolution to use for molecular replacement and separately what resolution to use for model rebuilding. If you specify "0.0" for resolution (recommended) then defaults will be used for molecular replacement (i.e. use data to 2.5A if available to solve structure, then carry out rigid body refinement of final solution with all data) and all the data will be used for model rebuilding. Composition of the asymmetric unit. PHASER needs to know what the total mass in the asymmetric unit is (i.e. not just the mass of the search models). You can define this either by specifying one or more protein or nucleic acid sequence files, or by specifying protein or nucleic acid molecular masses, and telling the Wizard how many copies of each are present. Space groups to search. You can request that all space groups with the same point group as the one you start out with be searched, and the best one be chosen. If you select this option then the best space group will be used for model rebuilding in AutoBuild. Ensembles to search for. AutoMR builds up a model by finding a set of good positions and orientations of one "ensemble", and then using each of those placements as starting points for finding the next ensemble, until all the contents of the asymmetric unit are found and a consistent solution is obtained. You can specify any number of different ensembles to search for, and you can search for any number of copies of each ensemble. The order of searching for ensembles makes a difference, but Phaser chooses a sensible default search order based on the size and assumed accuracy of the different ensembles. In difficult cases you could try permuting the search order. Each ensemble can be specified by a single PDB file or a set of PDB files. The contents of one set of PDB files for an ensemble must all be oriented in the same way, as they will be put together and used as a group always in the molecular replacement process. You will need to specify how similar you think each input PDB file that is part of an ensemble is to the structure that is in your crystal. You can specify either sequence identity, or expected rmsd. Note that if you use a homology model, you should give the sequence identity of the template from which the model was constructed, not the 100% identity of the model! Output files from AutoMRWhen you run AutoMR the output files will be in a subdirectory with your run number: AutoMR_run_1_/ # subdirectory with results
Model rebuilding. After PHASER molecular replacement the AutoMR Wizard loads the AutoBuild Wizard and sets the defaults based on the MR solution that has just been found. You can use the default values, or you may choose to use 2Fo-Fc maps instead of density-modified maps for rebuilding, or you may choose to start the model-rebuilding with the map coefficients from MR.1.mtz. How to run the AutoMR WizardRunning the AutoMR Wizard is easy. For example, from the command-line you can type: phenix.automr native.sca search.pdb RMS=0.8 mass=23000 copies=1 The AutoMR Wizard will find the best location and orientation of the search model search.pdb in the unit cell based on the data in native.sca, assuming that the RMSD between the correct model and search.pdb is about 0.8 A, that the molecular mass of the true model is 23000 and that there is 1 copy of this model in the asymmetric unit. Once the AutoMR Wizard has found a solution, it will automatically call the AutoBuild Wizard and rebuild the model. Components, copies, search models, and ensembles
What the AutoMR wizard needs to runIn a simple case where you have one search model and are looking for N copies of this model in your structure, you need:
It may be advantageous to search using an ensemble of similar structures, rather than a single structure. If you have an ensemble of search models to search for, then specify it as coords="model_1.pdb" coords="model_2.pdb" coords="model_3.pdb" In this case you need to give the RMS or identity for each model: identity='45 40 35'. Each of the models in the ensemble must be in the same orientation as the others, so that the ensemble of models can be placed as a group in the unit cell. You may also use phenix.ensembler to generate a single multi-model PDB file containing the entire ensemble. In this case you should specify a single overall RMS or identity for the ensemble. Running from a parameters fileYou can run phenix.automr from a parameters file. This is often convenient because you can generate a default one with: phenix.automr --show_defaults > my_automr.effand then you can just edit this file to match your needs and run it with: phenix.automr my_automr.eff If you are searching for more than one ensemble, or if there is more than one component in the a.u., then use a parameters file and specify them like this (put all of this in a file like "my_mr.eff" and run it with "phenix.automr my_mr.eff":
automr {
ensemble {
ensembleID = "mol1"
copies_to_find = 1
coords = mol1.pdb
identity = None
RMS = "0.85"
}
ensemble {
ensembleID = "mol2"
copies_to_find = 1
coords = mol2.pdb
identity = None
RMS = "0.90"
}
component {
seq_file = "seq1.dat"
component_type = *protein nucleic_acid
mass = None
component_copies = 1
}
component {
seq_file = "seq2.dat"
component_type = *protein nucleic_acid
mass = None
component_copies = 1
}
}
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 data.mtz has columns F SIGF then you might specify data=data.mtz input_label_string="F SIGF" You can find out all the possible label strings in a data file that you might use by typing: phenix.autosol display_labels=data.mtz # display all labels for data.mtz You 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 seq_file=seq.dat # sequence file ExamplesStandard AutoMR run with coords.pdb native.scaRun AutoMR using coords.pdb as search model, native.sca as data, assume RMS between coords.pdb and true model is about 0.85 A, the sequence of true model is seq.dat and there is 1 copy in the asymmetric unit: phenix.automr coords.pdb native.sca RMS=0.85 seq.dat copies=1 \
n_cycle_rebuild_max=2 n_cycle_build_max=2
Specifying data columnsRun AutoMR as above, but specify the data columns explicitly: phenix.automr coords.pdb RMS=0.85 seq.dat copies=1 \
data=data.mtz input_label_string="F SIGF" \
n_cycle_rebuild_max=2 n_cycle_build_max=2
Note that the data columns are specified by a string that includes both
F and SIGF : "F SIGF". The string must match some set of data labels
that can be extracted automatically from your data file.
You can find the possible values of this string as described above
with
phenix.automr display_labels=data.mtz Specifying a refinement file for AutoBuildRun AutoMR as above, but specify a refinement file that is different from the file used for the MR search: phenix.automr coords.pdb RMS=0.85 seq.dat copies=1 \
data=data.mtz input_label_string="F SIGF" \
input_refinement_file=refinement.mtz \
input_refinement_labels="FP SIGFP FreeR_flag" \
n_cycle_rebuild_max=2 n_cycle_build_max=2
Note that the commands input_refinement_file and input_refinement_labels are
in the scope "autobuild_variables" .
These commands and others with this prefix are
passed on to AutoBuild.
AutoMR searching for 2 componentsRun AutoMR on a structure with 2 components. Define the components of the asymmetric unit with sequence files (beta.seq and blip.seq) and number of copies of each component (1). Define the search models with PDB files and estimated RMS from true structures. This is all done by creating a parameters file with all the control information in it. Put all of this in a file like "my_mr.eff" and run it with "phenix.automr my_mr.eff":
automr {
data = "w1.sca"
build = False
ensemble {
ensembleID = "mol1"
copies_to_find = 1
coords = mol1.pdb
identity = None
RMS = "0.85"
}
ensemble {
ensembleID = "mol2"
copies_to_find = 1
coords = mol2.pdb
identity = None
RMS = "0.90"
}
component {
seq_file = "seq1.dat"
component_type = *protein nucleic_acid
mass = None
component_copies = 1
}
component {
seq_file = "seq2.dat"
component_type = *protein nucleic_acid
mass = None
component_copies = 1
}
}
Specifying molecular masses of 2 componentsRun AutoMR as in the previous example, except specify the components of the asymmetric unit with molecular masses (30000 and 20000), and define the search models with PDB files and percent sequence identity with the true structures (50% and 60%). This is again all done by creating a parameters file with all the control information in it. Put all of this in a file like "my_mr.eff" and run it with "phenix.automr my_mr.eff":
automr {
data = "w1.sca"
seq_file = seq.dat
ensemble {
ensembleID = "mol1"
copies_to_find = 1
coords = mol1.pdb
identity = 50
}
ensemble {
ensembleID = "mol2"
copies_to_find = 1
coords = mol2.pdb
identity = 60
}
component {
component_type = *protein nucleic_acid
mass = 30000
component_copies = 1
}
component {
component_type = *protein nucleic_acid
mass = 40000
component_copies = 1
}
autobuild_variables{
n_cycle_rebuild_max = 1
}
}
AutoMR searching for 2 components, but specifying the orientation of one of themRun AutoMR on a structure with 2 components. Define the components of the asymmetric unit with sequence files (beta.seq and blip.seq) and number of copies of each component (1). Define the search models with PDB files and estimated RMS from true structures. Define the orientation and position of one component. Define the number of copies to find for each component (0 for beta, which is fixed, 1 for blip). This is again all done by creating a parameters file with all the control information in it. Put all of this in a file like "my_mr.eff" and run it with "phenix.automr my_mr.eff":
automr {
data = "w1.sca"
seq_file = seq.dat
ensemble {
ensembleID = "mol1"
copies_to_find = 1
coords = mol1.pdb
identity = 50
}
ensemble {
ensembleID = "mol2"
copies_to_find = 0
coords = mol2.pdb
identity = 60
}
component {
component_type = *protein nucleic_acid
mass = 30000
component_copies = 1
}
component {
component_type = *protein nucleic_acid
mass = 40000
component_copies = 1
}
autobuild_variables{
n_cycle_rebuild_max = 1
}
fixed_ensembles {
fixed_ensembleID_list="mol2"
fixed_euler_list = 199.84 41.535 184.15
fixed_frac_list = -0.49736 -0.15895 -0.28067
}
}
Note: you have to define an ensemble for the fixed molecule (mol2 in this
example) and that you search for 0 copies of this molecule.
Possible ProblemsSpecific limitations and problems
Literature
Additional informationList of all AutoMR 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
-------------------------------------------------------------------------------
automr
build= True Run AutoBuild immediately after AutoMR
data= None Datafile (any standard format) Structure factor amplitudes will
be taken from this file.
copies= None Set both copies_to_find and component_copies with copies. This
is the number of copies of this search model to find, and also the
number of copies of this sequence or mass in the asymmetric unit.
ensembleID= None Optional ID for ensemble
copies_to_find= None Number of copies of this ensemble to find in a.u.
coords= None model(s) for this ensemble.
identity= None Percent identity(ies) of model(s) in this ensemble to
structure (alternative is RMS). Should be a space- or
comma-separated list of numbers between 0 and 100.
RMS= None RMSD(s) of model(s) to structure (alternative is identity).
Should be a space- or comma-separated list of numbers, typically
between 0.8 and 2.0, but occasionally higher.
seq_file= None protein seq_file for this component.
component_type= *protein nucleic_acid protein or nucleic acid.
mass= None molecular mass (Da) of this component.
component_copies= None Number of copies of this component in the a.u.
(required). (Command-ine only)
crystal_info
unit_cell= None Enter cell parameter a b c alpha beta gamma
chain_type= *Auto PROTEIN DNA RNA You can specify whether to build
protein, DNA, or RNA chains. At present you can only build
one of these in a single run. If you have both DNA and
protein, build one first, then run AutoBuild again,
supplying the prebuilt model in the
"input_lig_file_list" and build the other. NOTE:
default for this keyword is Auto, which means " carry
out normal process to guess this keyword". The process
is to look at the sequence file and/or input pdb file to see
what the chain type is. If there are more than one type, the
type with the larger number of residues is guessed. If you
want to force the chain_type, then set it to PROTEIN RNA or
DNA.
resolution= 0 Enter the high-resolution limit for MR search. All the
data input will be written out regardless of your choice. By
default, the final rigid-body refinement will use all data.
space_group= None Space Group symbol (i.e., C2221 or C 2 2 21)
input_files
input_label_string= None Choose the set of labels that represent the F
and sigma columns for your data. NOTE: Applies to
input data file for AutoMR. See also 'input_labels',
which applies to input data file for AutoBuild.
ensemble An ensemble is one or more models, already superimposed, to be
used as a search model. You need to specify the coordinates (list
of PDB files), how many copies to find, and either the percent
identity of the search model(s) to the actual structure OR
estimates of the RMS coordinate differences.
ensembleID= "ensemble_1" ID for this ensemble.
copies_to_find= None Number of copies of this ensemble to find in a.u.
coords= None model(s) for this ensemble.
identity= None percent identity(ies) of model(s) in this ensemble to
structure (alternative is RMS).
RMS= None RMSD(s) of model(s) to structure (alternative is identity).
added_ensemble= False Used internally to flag if this ensemble was added
automatically
component The components are the contents of the asymmetric unit. They help
Phaser figure out how much scattering is there. You need to
specify for each component (1) whether it is protein or nucleic
acid, (2) the molecular mass of the component OR the sequence,
and (3) how many of them there are,
componentID= None ID for this component.
seq_file= None protein seq_file for this component.
component_type= *protein nucleic_acid protein or nucleic acid.
mass= None molecular mass (Da) of this component.
component_copies= None Number of copies of this component in the a.u.
(required). (Command-ine only)
added_component= False Used internally to flag if component was added
automatically
decision_making
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.
overlap_allowed= None Solutions will be accepted by default if fewer
than 5 percent of residues are involved in clashes. You
can choose to increase the percent clashes if the
packing is tight and your search molecule is not
exactly the same as the molecule in the cell.
selection_criteria_rot= *Percent_of_best Number_of_solutions Z_score All
Choose a criterion for keeping rotation
solutions at each stage. The choices are:
Percent of Best Score: AutoMR looks down the
list of LLG scores and only keeps the ones that
differ from the mean by more than the chosen
percentage, compared to the top solution. Number
of Solutions: Keep the N top solutions (you can
set N; default=1) Z-score: Keep all the
solutions with a Z-score greater than X (you can
set X; default=6). All: Keep everything and go
on holiday while Phaser crunches through it all
(definitely not recommended!)
selection_criteria_rot_value= 75 Choose a value for your criterion for
keeping rotation solutions at each stage.
Percent of Best Score: AutoMR looks down
the list of LLG scores and only keeps the
ones that differ from the mean by more
than the chosen percentage, compared to
the top solution. Enter your desired
percentage into the entry field
(default=75%) Number of Solutions: Keep
the N top solutions (you can set N;
default=1) Z-score: Keep all the solutions
with a Z-score greater than X (you can set
X; default=6). All: Keep everything and go
on holiday while Phaser crunches through
it all (definitely not recommended!)
fast_search_mode= None Run phaser with selection_criteria_rot_value and
then if no obvious solution, repeat with cutoff
lowered by search_down_percent. If None, then use
Phaser default.
search_down_percent= 25 Used if fast_search_mode=True. Run phaser with
selection_criteria_rot_value and then if no obvious
solution, repeat with cutoff lowered by
search_down_percent
do_anisotropy_correction= True Choose whether you want to apply
anisotropy correction
all_plausible_sg_list= None Choose which space groups are plausible
use_all_plausible_sg= False Often you will want to search all space
groups with the same point group as you may not
know which is correct from your data. Choose
use_all_plausible_sg=True to do this. NOTE: You
can also select which of space groups to consider
using all_plausible_sg_list'
check_inverse_hand= True Normally you do not know the hand of your space
group Choosing check_inverse_hand (default) will
tell Phaser to try both the space group you specify
and its inverse NOTE: compare with
use_all_plausible_sg=True which further expands the
search to all space groups with the same point-group
permute_search_order= False You can ask Phaser to try all permutations
of the order in which ensembles are searched
number_of_output_models= 1 Number of solutions to output
disable_check= False You can disable the consistency check for ensemble
mass
fixed_ensembles If you already know the placement of one or more molecules
you can specify them as fixed ensembles.
fixed_ensembleID_list= None Enter the ID (set with ensemble_1.ensembleID
or equivalent) of the component that is to be
fixed. NOTE 1: Each ensemble in
fixed_ensembleID_list must be defined. NOTE 2:
you can enter more than one fixed component if
you want. If you do, then enter fixed_euler_list
in multiples of 3 numbers and also
fixed_frac_list in multiples of 3 numbers.
fixed_euler_list= 0.0 0.0 0.0 Enter Euler angles (from AutoMR or Phaser)
for fixed component defined with
fixed_ensembleID_list. NOTE 2: you can enter more than
one fixed component if you want. If you do, then enter
fixed_euler_list in multiples of 3 numbers and also
fixed_frac_list in multiples of 3 numbers.
fixed_frac_list= 0.0 0.0 0.0 Enter fractional offset (location) for
fixed component (from AutoMR or Phaser) for fixed
component defined with fixed_ensembleID_list. NOTE 2:
you can enter more than one fixed component if you
want. If you do, then enter fixed_euler_list in
multiples of 3 numbers and also fixed_frac_list in
multiples of 3 numbers.
fixed_frac_list_is_fractional= True Normally fixed_frac_list is
fractional coordinates. You can say
fixed_frac_list_is_fractional=False to
instead use orthogonal angstroms to
specify the locations of your ensembles.
model_building If you specify "build=True" then AutoBuild will be
run right after molecular replacement. You may wish to set
"rebuild_in_place" to True or False if you do not
wish for this to be chosen automatically (Rebuild-in-place
will not add or delete residues, if you set it to False it
will try to rebuild your model from scratch.
build_type= *RESOLVE RESOLVE_AND_BUCCANEER You can choose to build
models with RESOLVE or RESOLVE and BUCCANEER 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
resolution_build= 0 Enter the high-resolution limit for model-building.
If 0.0, the value of resolution is used as a default.
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.
autobuild_variables
two_fofc_in_rebuild= None Actively sets two_fofc_in_rebuild in
AutoBuild. NOTE: value is not checked
include_input_model= None Actively sets include_input_model in
AutoBuild. NOTE: value is not checked
n_cycle_rebuild_min= None Actively sets n_cycle_rebuild_min in
AutoBuild. NOTE: value is not checked
n_cycle_rebuild_max= None Actively sets n_cycle_rebuild_max in
AutoBuild. NOTE: value is not checked
n_cycle_build_min= None Actively sets n_cycle_build_min in AutoBuild.
NOTE: value is not checked
n_cycle_build_max= None Actively sets n_cycle_build_max in AutoBuild.
NOTE: value is not checked
rebuild_in_place= None Actively sets rebuild_in_place in AutoBuild.
NOTE: value is not checked
thorough_denmod= None Actively sets thorough_denmod in AutoBuild. NOTE:
value is not checked
start_chains_list= None Actively sets start_chains_list in AutoBuild.
NOTE: value is not checked
input_refinement_file= None Actively sets input_refinement_file in
AutoBuild. NOTE: value is not checked
input_refinement_labels= None Actively sets input_refinement_labels in
AutoBuild. NOTE: value is not checked
input_labels= None Actively sets input_labels in AutoBuild. NOTE: value
is not checked
resolve_command_list= None Actively sets resolve_command_list in
AutoBuild. NOTE: value is not checked
resolve_pattern_command_list= None Actively sets
resolve_pattern_command_list in AutoBuild.
NOTE: value is not checked
morph= None Actively sets morph in AutoBuild. NOTE: value is not checked
morph_rad= None Actively sets morph_rad in AutoBuild. NOTE: value is not
checked
general
nbatch= 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.
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.
keep_files= overall_best*.pdb overall_best*.mtz List of files that are
not to be cleaned up. wildcards permitted
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
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 Not presently applicable to automr
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 like this: input_label_string="FP SIGFP
" # each individual label counts
dry_run= False Just read in and check parameter names
params_only= False Just read in and return parameter defaults
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
sg= None Obsolete. Use space_group instead
composition_num_list= 1 Number of copies of this component. Not for
general use.
weight_list= 0.0 Molecular weight of component (Da; e.g. 30000) . Not
for general use.
weight_seq_list= Prot_seq_file Choose whether to define composition
through molecular weight or sequence. Choices are
"MW_protein","MW_nucleic",
"Prot_seq_file","Nucl_seq_file" Not
for general use
input_data_file= None Not normally used. Use "data=" instead
input_pdb_file= None Not normally used. Use "coords=" instead
input_seq_file= None Not normally used. Use "seq_file=" instead
input_seq_file_list= None Not normally used. Use
"component.seq_file" instead
rebuild_after_mr= True Not normally used. Use instead
"build=True"
solution_key= MR Prefix for name of pdb files output
build_gui= True If checked, the AutoBuild GUI will automatically launch
after AutoMR is finished, with input files pre-loaded.
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