Automated ligand fitting with LigandFit




Purpose of the LigandFit Wizard

The LigandFit Wizard carries out fitting of flexible ligands to electron density maps.


The LigandFit 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 LigandFit Wizard works

The LigandFit wizard provides a command-line and graphical user interface allowing the user to identify a datafile containing crystallographic structure factor information, an optional PDB file with a partial model of the structure without the ligand, and a PDB file containing the ligand to be fit (in an allowed but arbitrary conformation).

The wizard checks the data files for consistency and then calls RESOLVE to carry out the fitting of the ligand into the electron-density map. The best map to use is usually a 2Fo-Fc map from phenix.refine. You can also have LigandFit calculate a difference map, with F=FP-FC. It can also be an Fobs map (calulated from FP with phases PHIC from the input partial model), or an arbitrary map, calculated with FP PHI and optional FOM. If you supply an input partial model, then the region occupied by the partial model is flattened in the map used to fit the ligand, so that the ligand will normally not get placed in this region.

The ligand fitting is done by RESOLVE in a three-stage process. First, the largest contiguous region of density in the map not already occupied by the model is identified. The ligand will be placed in this density. (If desired, the location of the ligand can instead be defined by the user as near a certain residue or near specified coordinates. ) Next, many possible placements of the largest rigid sub-fragments of the ligand are found within this region of high density. Third, each of these placements is taken as a starting point for fitting the remainder of the ligand. All these ligand fits are scored based on the fit to the density, and the best-fitting placement is written out.

The output of the wizard consists of a fitted ligand in PDB format and a summary of the quality of the fit. Multiple copies of a ligand can be fit to a single map in an automated fashion using the LigandFit wizard as well.

How to run the LigandFit Wizard

Running the LigandFit Wizard is easy. For example, from the command-line you can type:

phenix.ligandfit data=datafile.mtz model=partial_model.pdb ligand=ligand.pdb

The LigandFit Wizard will carry out ligand fitting of the ligand in ligand.pdb based on the structure factor amplitudes in datafile.mtz, calculating phases based on partial-model.pdb. All rotatable bonds will be identified and allowed to take stereochemically reasonable orientations.

What the LigandFit wizard needs to run

The ligandfit wizard needs:

The ligand file can be a PDB file with 1 stereochemically acceptable conformation of your ligand. It can alternatively be a file containing a SMILES string, in which case the starting ligand conformation will be generated with the PHENIX elbow routine. It can also be a 3-letter code that specifies a ligand in the Chemical Components Dictionary of the PDB, in which case the ligand is taken from that dictionary with idealized geometry.

The command_line ligandfit interpreter will guess which file is your data file but you have to tell it which file is the model and which is the ligand.

Specifying which columns of data to use from input data files

If 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 FP SIGFP then you might specify

input_labels="FP SIGFP"

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 file
partial_model=coords.pdb  # starting model without ligand
ligand=ligand.pdb # any stereochemically allowed conformation of your ligand
resolution=3     # dmin of 3 A
quick=False      # specify if you want to look hard for a good conformation
ligand_cc_min=0.75   # quit if the CC of ligand to map is 0.75 or better
number_of_ligands=3  # find 3 copies of the ligand
n_group_search=3     # try 3 different fragments of the ligand in initial search
ligand_start=side.pdb # build ligand superimposing on side.pdb

Output files from LigandFit

When you run LigandFit the output files will be in a subdirectory with your run number:

LigandFit_run_1_/   # subdirectory with results
LigandFit_summary.dat  # overall summary
LigandFit_Facts.dat   # all Facts about the run
LigandFit_warnings.dat  # any warnings

Running from a parameters file

You can run phenix.ligandfit from a parameters file. When you run ligandfit a parameters file is written in the output directory. Then you can edit this file and run it with:

phenix.ligandfit  my_ligandfit.eff


Sample command_line inputs

phenix.ligandfit model=partial.pdb ligand=ATP \
phenix.ligandfit data=perfect.mtz \
 lig_map_type=pre_calculated_map_coeffs \
   model=partial.pdb ligand=NAD
phenix.ligandfit model=partial.pdb ligand=ATP quick=True

If your refine a model with a command such as,

phenix.refine data.mtz partial.pdb

then you will end up with the refined model,


and a map coefficients file:


You can then run ligandfit using the 2Fo-Fc map calculated from these map coefficients:

phenix.ligandfit data=partial_refine_001_map_coeffs.mtz \
 model=partial_refine_001.pdb ligand=NAD quick=True

or if you want to specify the coefficients explicitly you can add the column labels:

phenix.ligandfit data=partial_refine_001_map_coeffs.mtz  \
model=partial_refine_001.pdb ligand=GOL quick=True \
input_labels="2FOFCWT PH2FOFCWT"

For a difference map from the same file you can say:

phenix.ligandfit data=partial_refine_001_map_coeffs.mtz  \
 model=partial_refine_001.pdb ligand=AMP quick=True \
 input_labels="FOFCWT PHFOFCWT"
phenix.ligandfit model=partial.pdb \
  ligand=ligand_list.dat file_or_file_list=file_with_list_of_files

Note that you have to specify


or else the Wizard will try to interpret the contents of ligand_list.dat as a SMILES string. Here the "file_with_list_of_files" is a flag, not something you substitute with an actual file name. You use it just as listed above.

phenix.ligandfit model=partial.pdb ligand=ADP \
   ligand_near_chain="A" ligand_near_res=92
phenix.ligandfit model=partial.pdb ligand=GTP \

NOTE: the file start.pdb must contain an entire rigid group of atoms (so that ligandfit can identify the position and orientation of at least one rigid part of the ligand.)

phenix.ligandfit model=partial.pdb ligand=GTP \

R-free flags and test set

In Phenix the parameter test_flag_value 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 and you do not need to do anything special. 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.

Possible Problems

Specific limitations and problems


Ligand identification using electron-density map correlations. T.C. Terwilliger, P.D. Adams, N.W. Moriarty, and J.D. Cohn. Acta Crystallogr D Biol Crystallogr 63, 101-7 (2006). Automated ligand fitting by core-fragment fitting and extension into density. T.C. Terwilliger, H. Klei, P.D. Adams, N.W. Moriarty, and J.D. Cohn. Acta Crystallogr D Biol Crystallogr 62, 915-22 (2006).

List of all available keywords