Guided Ligand Replacement
- Overview
- Input files
- Output files
- References
- List of all guided_ligand_replacement keywords
Overview
The Guided Ligand Replacement (GLR) tool is designed to use prior
knowledge from a previously fit ligand to expedite the fitting of a
"similar" ligand into the same or "similar" protein. The similarity
required between the pair of ligands can be as little as a few atoms.
The proteins are overlayed using phenix.superpose_pdbs. The ligands
are matched using the electronic Ligand Builder and Optimization
Workbench (eLBOW) via another tool called phenix.superpose_ligands.
Once the ligand has been fit, a Real-Space Refinement (RSR) is
performed and the final model written to disk.
Input files
GLR requires a number of inputs and also has some options, all of which
are provided using the phil formalism. The list of
required inputs:
- guide_pdb_file_name: this is a PDB file containing a model-ligand
model.
- protein_pdb_file_name: this is a file containing the protein
model of current interest into which the ligand is to be fit.
- map_coeffs_file_name: this is a maps coefficients file output from
a phenix.refine run.
The input for the ligand can be any input file that is readable by eLBOW.
Either or both of the following phil parameters can be used.
- ligand_input_file_name: this is a file containing chemical information
about the ligand.
- ligand_cif_file_name: this is the
of a ligand restraints file for the RSR step. If not supplied, the
restraints are generated from ligand_input_file_name.
Optional inputs include:
- ligand_selection_in_guide_model: this selects a ligand in the guiding
model. While GLR tries to make a sensible selection based on ligand code
or uniqueness, it may be necessary to make an explicit selection.
- phenix.superpose_pdbs: this allows selection of the same parameters
as in the standalone program.
Output files
By default, GLR will generate a PDB file with the fit ligand.
References
- Moriarty NW, Grosse-Kunstleve RW, Adams PD. electronic Ligand Builder
and Optimization Workbench (eLBOW): a tool for ligand coordinate and
restraint generation. Acta Cryst. 2009, D65:1074-1080.
List of all guided_ligand_replacement 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
-------------------------------------------------------------------------------
guided_ligand_replacement
input
guide_pdb_file_name= None PDB filename containing protein model and fit
ligand
protein_pdb_file_name= None PDB file containing protein but not a ligand
ligand_input_file_name= None File contains chemical input of a ligand
data_file_name= None Amplitudes or intensities
map_coeffs_file_name= None Map coefficients from a refinement of the apo
model
ligand_cif_file_name= None This restraints file will be used for the
real space refinement. If not suplied, a set of
restraints are generated from the ligand input.
ligand_selection_in_guide_model= None The specific ligand to use from
the guide structure
real_space_refinement= lockit *ideal off
real_space_refinement_selection_radius= 5.
output
file_name= None Defaults to current directory
job_title= None Job title in PHENIX GUI, not used on command line
superpose_pdbs
input
pdb_file_name_protein= None Name of PDB file with model to fit to
pdb_file_name_guide= None Name of PDB file with model that will be
fit to pdb_file_name_protein
alignment Set of parameters for sequence alignment. Defaults are good
for most of cases
alignment_style= local *global
gap_opening_penalty= 1
gap_extension_penalty= 1
similarity_matrix= blosum50 dayhoff *identity
validation
rmsd_cutoff= 2.
similarity_cutoff= 80.
superpose_ligands
quick= True
lockit_parameters
lbfgs_max_iterations= 500
finishing_geometry_minimization
cycles_max= 100
first_weight_scale= 0.1
cycle_weight_multiplier= 1.0
superpose_cycle_end_with_cycle_start= False
dihedral_restraints= False
output_file= Auto
real_space_target_weights
first_sample= 10
sampling_step= 30
number_of_samples= 10
bond_rmsd_target= 0.03
worst_acceptable_bond_rmsd
pool_size= 10
max_pool_average= 0.1
|