Finding all ligands in a map with phenix.find_all_ligands

Author(s)

phenix.find_all_ligands: Tom Terwilliger

Purpose

phenix.find_all_ligands is a command line tool for finding all the ligands in a map by repetitively running phenix.ligandfit with a series of ligands and choosing the best-fitting one at each cycle.

Usage

How phenix.find_all_ligands works:

The basic procedure for phenix.find_all_ligands has three steps. The first is to identify the largest contiguous region of density in your map that is not already occupied by your model or previously-fitted ligands. The second is to fit each ligand (you identify the candidate ligands in advance) into this density. The third is to choose the one that fits the density the best. Then the best-fitting ligand is added to the structure and the process is repeated until the number of ligands you request is found or the correlation of ligand to the map drops below the value you specify (default=0.5).

Output files from phenix.find_all_ligands

The output ligand files from phenix.find_all_ligands are normally in the temporary directory (default='temp_dir'). They will be files with names such as "SITE_1_ATP.pdb" for the placement of ATP in the first site fitted.

Examples

Standard run of phenix.find_all_ligands:

Running phenix.find_all_ligands is easy. Usually you will want to edit a small parameter file (find_all_ligands.eff) to contain your commands like this, where the ligandfit commands are sent to phenix.ligandfit: for the actual fitting and the find_all_ligands commands determine what searches are done: type:

#  commands for running phenix.find_all_ligands
find_all_ligands {
  number_of_ligands = 5
  cc_min = 0.5
  ligand_list =  ATP.pdb NAD.pdb
  nproc = 2
}
ligandfit {
  data = "nsf-d2.mtz"
  model = "nsf-d2_noligand.pdb"
  lig_map_type = fo-fc_difference_map
}

You might also want to add to this some additional commands for phenix.ligandfit. Any commands for ligandfit are allowed, except that the commands "ligand" and "input_lig_file" are ignored as the input ligand comes from the find_all_ligands command "ligand_list":

# find_all_ligands.eff  more commands for ligandfit
ligandfit {
data = "nsf-d2.mtz"
model = "nsf-d2_noligand.pdb"
lig_map_type = fo-fc_difference_map
ligand_cc_min = 0.75
verbose = Yes
}

where you can put any phenix.ligandfit commands in the braces.

Then you can run this with the command:

phenix.find_all_ligands find_all_ligands.eff

Possible Problems

Specific limitations and problems:

This method uses phenix.ligandfit to do the ligand fitting, so all the commands, features, and limitations of phenix.ligandfit apply to phenix.find_all_ligands.

Literature

Additional information

NOTE: in addition to the find_all_ligands keywords shown here, all phenix.ligandfit commands are also allowed, except that the commands "ligand" and "input_lig_file" are ignored as the input ligand comes from the find_all_ligands.

List of all available keywords

find_all_ligands
- number_of_ligands = None Total number of ligand sites. Ignored if "None". find_all_ligands will keep looking until the correlation coefficient for the fit of the best ligand is less than cc_min or the number of ligands placed is number_of_ligands, whichever comes first
- cc_min = 0.50 Ignored if "None". find_all_ligands will keep looking until the correlation coefficient for the fit of the best ligand is less than cc_min or the number of ligands placed is number_of_ligands, whichever comes first
- ligand_list = None List of files with ligands to find
- nproc = 1 number of processors to use
- background = True run jobs in background or not (if nproc is greater than 1)
- run_command = "sh " Command for running jobs (e.g., sh or qsub )
- verbose = False verbose output
- raise_sorry = False Raise sorry if problems
- debug = False debugging output
- temp_dir = Auto Optional temporary work directory
- output_dir = "" Output directory where files are to be written
- dry_run = False Just read in and check parameter names
- check_wait_time = 1.0 You can specify the length of time (seconds) to wait between checking for subprocesses to end
- 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:....
ligandfit
- data = None Datafile. This can be any format if only FP is to be read in. If phases are to be read in then MTZ format is required. The Wizard will guess the column identification. If you want to specify it you can say input_labels="FP" , or input_labels="FP PHIB FOM".
- ligand = None Three-letter code of ligand, or file containing information about the ligand (PDB or SMILES)
- model = None PDB file with model for everything but the ligand
- quick = False Set to True for running as quickly as possible.
- crystal_info
  - unit_cell = None Enter cell parameter a b c alpha beta gamma
  - resolution = 0 High-resolution limit. Zero means keep everything. If map_in is specified, resolution must be given.
  - space_group = None Space Group symbol (i.e., C2221 or C 2 2 21)
- file_info
  - file_or_file_list = *single_file file_with_list_of_files Choose if you want to input a single file with PDB or other information about the ligand or if you want to input a file containing a list of files with this information for a list of ligands
  - input_labels = None Labels for input data columns
  - lig_map_type = fo-fc_difference_map fobs_map *pre_calculated_map_coeffs Enter the type of map to use in ligand fitting fo-fc_difference_map: Fo-Fc difference map phased on partial model (requires FOBS in your input file) fobs_map: Fo map phased on partial model (requires FOBS in your input file) pre_calculated_map_coeffs: map calculated from FP PHIB [FOM] coefficients in input data file (or 2FOFCWT PH2FOFCWT coeffs) If you supply a map just leave this at pre_calculated_map_coeffs.
  - ligand_format = *PDB SMILES Enter whether the files contain SMILES strings or PDB formatted information
- input_files
  - existing_ligand_file_list = None You can enter a list of PDB files with ligands you have already fit. These will be used to exclude that region from consideration.
  - ligand_start = None LigandFit will attempt to put your ligand superimposing on ligand_start if supplied. This must have some of the same atoms as your ligand, but does not have to have all of them.
  - ncs_in = None You can supply a file with NCS information for use with ligands_from_ncs
  - input_ligand_compare_file = None If you enter a PDB file with a ligand in it, the coordinates of the newly-built ligand will be compared with the coordinates in this file.
  - cif_def_file_list = None You can supply cif files for real-space refinement after fitting
  - refinement_file = None You can supply a file for full refinement containing F/I SIGF/SIGI FreeR_flag If you supply this file then after real-space refinement a round of full refinement will be carried out with phenix.refine
  - fobs_labels = None Labels for Fobs SigFobs or Iobs SigIobs for refinement_file... same format as for phenix.refine
  - r_free_label = None Label for FreeR_flag in refinement_file...same format as for phenix.refine
  - map_in = None Map file (alternative to data file). Can be .ccp4, .map, .mrc and will be converted to map coefficients before use.
- search_parameters
  - fixed_ligand = False Use fixed ligand (no rotations of any bonds) if set
  - conformers = 1 Enter how many conformers to create. If greater than 1, then ELBOW will always be used to generate them. If 1 then ELBOW will be used if a PDB file is not specified. These conformers are used to identify allowed torsion angles for your ligand. The alternative is to use the empirical rules in RESOLVE. ELBOW takes longer but is more accurate.
  - group_search = 0 Enter the ID number of the group from the ligand to use to seed the search for conformations
  - ligand_cc_min = 0.75 Enter the minimum correlation coefficient of the ligand to the map to quit searching for more conformations
  - ligand_completeness_min = 1 Enter the minimum completeness of the ligand to the map to quit searching for more conformations
  - local_search = True If local_search is True then, only the region within search_dist of the point in the map with the highest local rmsd will be searched in the FFT search for fragments
  - search_dist = 10 If local_search is True then, only the region within this distance of the point in the map with the highest local rmsd will be searched in the FFT search for fragments
  - use_cc_local = False You can specify the use of a local correlation coefficient for scoring ligand fits to the map. If you do not do this, then the region over which the ligand is scored are all points within 2.5 A of the atoms in the ligand. If you do specify use_cc_local, then the region over which the ligand is scored are all these points, plus all the contingous points that have density greater than 0.5 * sigma .
  - ligands_from_ncs = False You can try to use ncs (from your partial model file or from your ncs_in file) along with any ligands already found to place additional copies of your ligand. Only applicable if there is one type of ligand.
  - max_ligands_from_ncs = 1 You can specify how many of the ligands already found to consider using NCS (usually 1)
  - n_group_search = 3 Enter the number of different fragments of the ligand that will be looked for in FFT search of the map
  - n_indiv_tries_max = 10 If 0 is specified, all fragments are searched at once otherwise all are first searched at once then individually up to the number specified
  - n_indiv_tries_min = 5 If 0 is specified, all placements of a fragment are tested at once otherwise all are first tested at once then individually up to the number specified
  - number_of_ligands = 1 Number of copies of the ligand expected in the asymmetric unit
  - offsets_list = 7 53 29 You can specify an offset for the orientation of the templates in searching for ligands. This is used in generating diversity in models.
  - refine_ligand = True You can carry out real-space refinement on the ligand after fitting
  - ligand_occupancy = 1.0 You can set the initial occupancy of the ligand
  - real_space_target_weight = 10. You can carry change the weight on the real-space term in real-space refinement on the ligand after fitting
  - fittingParameters for tracing ligand
    - delta_phi_ligand = 40 Specify the angle (degrees) between successive tries in FFT search for fragments
    - fit_phi_inc = 20 Specify the angle (degrees) between rotations around bonds
    - fit_phi_range = -180 180 Range of bond rotation angles to search
- search_target
  - ligand_near_chain = None You can specify where to search for the ligand either with search_center or with ligand_near_res and ligand_near_chain. If you set ligand_near_chain="None" or leave it blank or do not set it, then all chains will be included. The keywords ligand_near_res and ligand_near_chain refer to residue/chain in the file defined by input_partial_model_file (or model if running from command line).
  - ligand_near_res = None You can specify where to search for the ligand either with search_center or with ligand_near_res and ligand_near_chain The keywords ligand_near_res and ligand_near_chain refer to residue/chain in the file defined by input_partial_model_file (or model if running from command line).
  - ligand_near_pdb = None You can specify where LigandFit should look for your ligands by providing a PDB file containing one or more copies of the ligand. If you want you can provide a PDB file with ligand+ macromolecule and specify the ligand name with name_of_ligand_near_pdb.
  - name_of_ligand_near_pdb = None You can specify where LigandFit should look for your ligands by providing a PDB file containing one or more copies of the ligand. If you want you can provide a PDB file with ligand+ macromolecule and specify the ligand name with name_of_ligand_near_pdb.
  - search_center = 0.0 0.0 0.0 Enter coordinates for center of search region (ignored if [0.,0.,0.])
- general
  - 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.
  - ligand_id = None You can specify an integer value for the ID of a ligand... This number will be added to whatever residue number the ligand search model in input_lig_file has. The keyword is only valid if a single copy of the ligand is to be found.
  - nbatch = 5 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
  - resolve_command_list = None Commands for resolve. One per line in the form: keyword value (put in the quotes.) 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.
  - 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.
  - check_wait_time = 1.0 You can specify the length of time (seconds) to wait between checking for subprocesses to end
  - 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.
  - queue_commands = None You can add any commands that need to be run for your queueing system. These are written before any other commands in the file that is submitted to your queueing system. For example on a PBS system you might say: queue_commands='#PBS -N mr_rosetta' queue_commands='#PBS -j oe' queue_commands='#PBS -l walltime=03:00:00' queue_commands='#PBS -l nodes=1:ppn=1' NOTE: you can put in the characters '<path>' in any queue_commands line and this will be replaced by a string of characters based on the path to the run directory. The first character and last two characters of each part of the path will be included, separated by '_',up to 15 characters. For example 'test_autobuild/WORK_5/AutoBuild_run_1_/TEMP0/RUN_1' would be represented by: 'tld_W_5_A1__TP0_1'
  - condor_universe = vanilla The universe for condor is usually vanilla. However you might need to set it to local for your cluster
  - add_double_quotes_in_condor = True You might need to turn on or off double quotes in condor job submission scripts. These are already default elsewhere but may interfere with condor paths.
  - condor = None Specifies if the group_run_command is submitting a job to a condor cluster. Set by default to True if group_run_command=condor_submit, otherwise False. For condor job submission mr_rosetta uses a customized script with condor commands. Also uses one_subprocess_level=True
  - 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
  - test_flag_value = Auto Normally leave this at Auto (default). This parameter sets the value of the test set that is to be free. Normally phenix sets up test sets with values of 0 and 1 with 1 as the free set. The CCP4 convention is values of 0 through 19 with 0 as the free set. Either of these is recognized by default in Phenix. If you have any other convention (for example values of 0 to 19 and test set is 1) then you can specify this with test_flag_value.
  - 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
  - local_temp_directory = None Write all temporary files to this directory and copy files specified by keep_files back to TEMP directory in working directory at the end of run. Used to speed up read/write operations. NOTE: Deletes all files except those specified by keep_files just like clean_up=True.
  - clean_up = None At the end of the entire run the TEMP directories will be removed if clean_up is True. Files listed in keep_files will not be deleted. If you want to remove files after your run is finished use a command like "phenix.autobuild run=1 clean_up=True"
  - print_citations = True Print citations at end of run
  - solution_output_pickle_file = None At end of run, write solutions to this file in output directory if defined
  - job_title = None Job title in PHENIX GUI, not used on command line
  - 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. 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
  - check_only = False Just read in and check initial parameters. Not for general use
  - keep_files = ligandfit*.pdb List of files that are not to be cleaned up. wildcards permitted
- display
  - number_of_solutions_to_display = None Number of solutions to put on screen and to write out
  - solution_to_display = 1 Solution number of the solution to display and write out ( use 0 to let the wizard display the top solution)
- run_control
  - 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 and AutoBuild like this: input_refinement_labels="FP SIGFP FreeR_flags" # each individual label counts
  - dry_run = False Just read in and check parameter names
  - params_only = False Just read in and return parameter defaults
  - display_all = False Just read in and display parameter defaults
  - coot = None Not presently applicable for ligandfit
- 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.
- 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
  - get_lig_volume = False You can ask to get the volume of the ligand and to then stop
  - input_data_file = None Not normally used. Use "data=" instead
  - input_lig_file = None Not normally used. Use "ligand=" instead.
  - ligand_code = None Not normally used. Use "ligand=" instead.
  - input_partial_model_file = None Not normally used. Use "model=" instead
  - cif_already_generated = False You can specify that the ligand cif file is already generated