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parKVFinder Manual
This is a comprehensive list of all PyMOL2 parKVFinder Tools, PyMOL parKVFinder Tools and parKVFinder command line interface commands.
This PyMOL plug-in is compatible with PyMOL v2.x.
Run parKVFinder: Executes parKVFinder. First, it checks the consistency of parKVFinder parameters. If any of these conditions fail, an appropriate warning message will be displayed. The cavity PDB file is loaded into the PyMOL viewer and the results information is displayed on the Results tab.
Show Grid: Creates a box of the search space for a target structure (selected on Input PDB combo box). It depends on Probe Out size and slightly on grid spacing (Step Size or Resolution options).
Save Parameters: Saves a parameters file (parameters.toml) to the current output directory without running parKVFinder.
Restore Default Values: Restores the initial values of all parameters at startup of PyMOL2 parKVFinder Tools.
Exit: Exits PyMOL2 parKVFinder Tools.
This tab features the main parameters and file paths for customizing parKVFinder's detection capabilities.
Input PDB: This combo box defines which structure will be used as input in parKVFinder execution. Its list is generated using molecular objects loaded in the PyMOL viewer.
Refresh: Refreshes the Input PDB list box of objects loaded in PyMOL viewer.
Resolution: Indirectly defines the grid spacing used in parKVFinder execution, which defines the number of voxels in the grid. There are three possible resolutions: Low (0.6 Å), Medium (0.50 Å) and High (0.25Å). Users can define only one grid spacing method (Step size or Resolution).
Step Size: Directly defines the grid spacing used in parKVFinder execution, which defines the number of voxels in the grid. Users can define only one grid spacing method (Step size or Resolution).
Probe In: A smaller probe that rolls around the target protein. Usually set to a water molecule (1.4 Å).
Probe Out: A larger probe that rolls around the target protein, which depending on the characteristics of the target structure, user may adjust probe size.
Removal Distance: Defines a distance to be removed from the cavity boundary. This length is converted to grid units by dividing it by grid spacing.
Volume Cutoff: Defines a filter to exclude cavities with smaller volumes than this limit. Useful to exclude uninteresting cavities from results.
Surface Representation: Selects surface type to be considered, Molecular Surface (VdW) or Solvent Accessible Surface (SAS).
Cavity Representation: Selects how parKVFinder exports its cavities PDB file. The Filled option exports all cavity points, and the Filtered option filters out some internal points before exporting cavities. This parameter affects the cavities visualization and memory requirement in PyMOL.
Output Base Name: This entry field defines the prefix of the output files (cavities PDB file, results file, parameters file and output directory name).
Output Directory: Path to a specific output directory where all files created by parKVFinder will be saved.
parKVFinder: Defines the path to the parKVFinder executable.
Dictionary: Defines the path to the parKVFinder van der Waals dictionary, which can be customized. The dictionary file contains the Van der Waals radii for atoms of the recognized residues. This file has a mandatory format:
--------------------------------------------------------------------------------
# This is a comment line
#>RES (residue name in 3 letter code)
#Atom_name\t\tAtom_radius
>ALA
N 1.8240
H 0.6000
HB1 1.4870
>ARG
CB 1.9080
HB2 1.4870
2HB 1.4870
>GEN
AC 2.00
AG 1.72
AL 2.00
--------------------------------------------------------------------------------
This tab features options for customizing parKVFinder's search space.
Box Adjustment: Checkbox that defines the search space to be considered, Whole Protein or Box Adjustment options. The Whole Protein mode (unckecked box) defines the search space as the target structure. The Box Adjustment mode (checked box) defines the search space as a custom box. When selecting the Box Adjustment mode, the Box Adjustment frame is enabled, which allows custom box adjustment.
Draw Box: Creates a box around a user selection - (sele) object. When the box object is drawn, Draw Box button is disabled.
Delete Box: Deletes the box object from PyMOL viewer and enable Draw Box button.
Redraw Box: Redraw box based on a user selection - (sele) object - and other box parameters (padding, minimum X, maximum X, minimum Y, maximum Y, minimum Z, maximum Z, angle 1 and angle 2). To customize the box, it is advisable to change one parameter at a time.
Padding: Defines padding around the selection which the box will be created.
Minimum/Maximum vertices: These entries adjust the box size. Each axis is associated with a color (red with X, green with Y and blue with Z). The base reference of the box is the vertex where the colored edges meet. Minimum vertices move the edge next to the base, while maximum vertices control the opposite side of the edge.
Angle 1: Rotates X axis.
Angle 2: Rotates Z axis.
Ligand Adjustment: When enabled, this mode limits the search space around a ligand. The ligand is defined in the Ligand PDB combo box, while the search radius is defined by the Ligand Cutoff entry.
Ligand PDB: This combo box defines which structure will be used as ligand in parKVFinder execution. Its list is generated using molecular objects loaded in the PyMOL viewer.
Refresh: Refreshes the Ligand PDB combo box of objects loaded in PyMOL viewer.
Ligand Cutoff: Defines the search radius from the ligand structure.
This tab displays parKVFinder results.
Results File: Path to result file.
Browse... Button to select a results file to load.
Load: Loads the information from results file.
Input File: Path to input PDB file.
Ligand File: Path to ligand PDB file.
Output File: Path to output PDB file.
Step Size: Results grid spacing.
Volume: Displays the calculated volume for each cavity, identified by a three-letter code. If the user selects a cavity, an active object is created in PyMOL viewer for visual inspection.
Surface Area: Displays the calculated surface area for each cavity, identified by a three-letter code. If the user selects a cavity, an active object is created in PyMOL viewer for visual inspection.
Interface Residues: Displays residues around the selected cavities on this list on an active object in the PyMOL viewer.
This PyMOL plug-in is compatible with PyMOL v1.8.x and PyMOL v2.x (legacy mode).
Run parKVFinder: Executes parKVFinder. First, it checks the consistency of parKVFinder parameters. If any of these conditions fail, an appropriate warning message will be displayed. The cavity PDB file is loaded into the PyMOL viewer and the results information is displayed on the Results Visualization tab.
Show Grid: Creates a box of the search space for a target structure (selected on Input PDB list box). It depends on Probe Out size and slightly on grid spacing (Step Size or Resolution options).
Save Parameters: Saves a parameters file (parameters.toml) to the current output directory without running parKVFinder.
Restore Default Values: Restores the initial values of all parameters at startup of PyMOL parKVFinder Tools.
Exit: Exits PyMOL parKVFinder Tools.
This tab features the main parameters and file paths for customizing parKVFinder's detection capabilities.
Input PDB: This list box defines which structure will be used as input in parKVFinder execution. The list is generated using molecular objects loaded in the PyMOL viewer.
Refresh List: Refreshes the Input PDB list box of objects loaded in PyMOL viewer.
Upload PDB: Loads a PDB file into PyMOL viewer and automatically refreshes the Input PDB list box.
Output Base Name: This entry field defines the prefix of the output files (cavities PDB file, results file, parameters file and output directory name).
Probe In: A smaller probe that rolls around the target protein. Usually set to a water molecule (1.4 Å).
Probe Out: A larger probe that rolls around the target protein, which depending on the characteristics of the target structure, user may adjust probe size.
Volume Cutoff: Defines a filter to exclude cavities with smaller volumes than this limit. Useful to exclude uninteresting cavities from results.
Removal Distance: Defines a distance to be removed from the cavity boundary. This length is converted to grid units by dividing it by grid spacing.
Step Size: Directly defines the grid spacing used in parKVFinder execution, which defines the number of voxels in the grid. Users can define only one grid spacing method (Step size or Resolution).
Resolution: Indirectly defines the grid spacing used in parKVFinder execution, which defines the number of voxels in the grid. There are three possible resolutions: Low (0.6 Å), Medium (0.50 Å) and High (0.25 Å). Users can define only one grid spacing method (Step size or Resolution).
Surface Representation: Selects surface type to be considered, Solvent Accessible Surface (SAS) or Molecular Surface (VdW).
Cavity Representation: Selects how parKVFinder exports its cavities PDB file. The Filled option exports all cavity points, and the Filtered option filters out some internal points before exporting cavities. This parameter affects the cavities visualization and memory requirement in PyMOL.
parKVFinder: Defines the path to the parKVFinder executable.
Dictionary: Defines the path to the parKVFinder van der Waals dictionary, which can be customized. The dictionary file contains the Van der Waals radii for atoms of the recognized residues. This file has a mandatory format:
--------------------------------------------------------------------------------
# This is a comment line
#>RES (residue name in 3 letter code)
#Atom_name\t\tAtom_radius
>ALA
N 1.8240
H 0.6000
HB1 1.4870
>ARG
CB 1.9080
HB2 1.4870
2HB 1.4870
>GEN
AC 2.00
AG 1.72
AL 2.00
--------------------------------------------------------------------------------
Output Directory: Path to a specific output directory where all files created by parKVFinder will be saved.
This tab features options for customizing parKVFinder's search space.
Search Procedure: Selects search space to be considered, Whole Protein or Box Adjustment options. The Whole Protein mode defines the search space as the target structure. The Box Adjustment mode defines the search space as a custom box. When selecting the Box Adjustment mode, a Box Adjustment frame is enabled, which allows custom box adjustment.
Draw Box: Creates a box around a user selection - (sele) object. When the box object is drawn, Draw Box button is disabled.
Delete Box: Deletes the box object from PyMOL viewer and enable Draw Box button.
Redraw Box: Redraw box based on a user selection - (sele) object - and other box parameters (padding, minimum X, maximum X, minimum Y, maximum Y, minimum Z, maximum Z, angle 1 and angle 2).
Padding: Defines padding around the selection which the box will be created.
Minimum/Maximum vertices: These entries adjust the box size. Each axis is associated with a color (red with X, green with Y and blue with Z). The base reference of the box is the vertex where the colored edges meet. Minimum vertices move the edge next to the base, while maximum vertices control the opposite side of the edge.
Angle 1: Rotates X axis.
Angle 2: Rotates Z axis.
Ligand Adjustment: When enabled, this mode limits the search space around a ligand. The ligand is defined in the Ligand PDB list box, while the search radius is defined by the Ligand Cutoff entry.
Ligand PDB: This list box defines which structure will be used as ligand in parKVFinder execution. The list is generated using molecular objects loaded in the PyMOL viewer.
Refresh List: Refreshes the Ligand PDB list box of objects loaded in PyMOL viewer.
Upload Ligand: Loads a PDB file into PyMOL viewer and automatically refreshes the Ligand PDB list box.
Ligand Cutoff: Defines the search radius from the ligand structure.
This tab displays parKVFinder results.
Results File: Button to select a results file to load.
Load: Loads the information from results file.
Input File: Path to input PDB file.
Ligand File: Path to ligand PDB file.
Output File: Path to output PDB file.
Step Size: Results grid spacing.
Volume: Displays the calculated volume for each cavity, identified by a three-letter code. If the user selects a cavity, an active object is created in PyMOL viewer for visual inspection.
Surface Area: Displays the calculated surface area for each cavity, identified by a three-letter code. If the user selects a cavity, an active object is created in PyMOL viewer for visual inspection.
Interface Residues: Displays residues around the selected cavities on this list on an active object in the PyMOL viewer.
parKVFinder command line interface handles the same parameters available in PyMOL2 parKVFinder Tools and PyMOL parKVFinder Tools, except for a different box adjustment treatment.
Note: If you are using parKVFinder for Windows (parKVFinder-win) version, instead of invoking the CLI using parKVFinder command, you must use %KVFinder_PATH%\parKVFinder-win64.exe command.
# Usage
parKVFinder <.pdb> [options]where <.pdb> is a path to a target PDB file.
All customizable options are set using short and/or long command line arguments.
List of options:
-
-hor--help: Display this help message.
# Usage
parKVFinder -h
parKVFinder --help-
-vor--version: Display parKVFinder version.
# Usage
parKVFinder -v
parKVFinder --version-
--verbose: Print extra information to stdout.
# Usage
parKVFinder <.pdb> --verbose-
-p <.toml>or--parameters <.toml>: Define path to parameters file.
# Usage
parKVFinder <.pdb> -p <.toml>
parKVFinder <.pdb> --parameters <.toml>-
-d <file>or--dictionary <file>: Define path to a custom dictionary file.
# Usage
parKVFinder <.pdb> -d <file>
parKVFinder <.pdb> --dictionary <file>Default: dictionary file in parKVFinder directory (KVFinder_PATH location).
The dictionary file contains the Van der Waals radii for atoms of the recognized residues. This file has a required format:
--------------------------------------------------------------------------------
# This is a comment line
#>RES (residue name in 3 letter code)
#Atom_name\t\tAtom_radius
>ALA
N 1.8240
H 0.6000
HB1 1.4870
>ARG
CB 1.9080
HB2 1.4870
2HB 1.4870
>GEN
AC 2.00
AG 1.72
AL 2.00
--------------------------------------------------------------------------------
-
-r <enum>or--resolution <enum>: Define resolution mode. Options include: Off, Low, Medium and High.
# Usage
parKVFinder <.pdb> -r <enum>
parKVFinder <.pdb> --resolution <enum>Default: Low.
-
-s <real>or--step <real>: Define step size (grid spacing).
# Usage
parKVFinder <.pdb> -s <real>
parKVFinder <.pdb> --step <real>-
-i <real>or--probe_in <real>: Define probe in size.
# Usage
parKVFinder <.pdb> -i <real>
parKVFinder <.pdb> --probe_in <real>Default: 1.4.
-
-o <real>or--probe_out <real>: Define probe out size.
# Usage
parKVFinder <.pdb> -o <real>
parKVFinder <.pdb> --probe_out <real>Default: 4.0.
-
--volume_cutoff <real>: Define cavities volume filter.
# Usage
parKVFinder <.pdb> --volume_cutoff <real>Default: 5.0.
-
--removal_distance <real>: Define removal distance when comparing probes surfaces.
# Usage
parKVFinder <.pdb> --removal_distance <real>Default: 2.4.
-
-tor--template: Create a parameter file template (parameters.toml) with defined parameters in the current working directory.
# Usage
parKVFinder <.pdb> -t
parKVFinder <.pdb> --template-
-Bor--box: Define a search box mode where parKVFinder will detect cavities.
# Usage
parKVFinder <.pdb> -B --<method> <file>
parKVFinder <.pdb> --box --<method> <file>-
--custom_box <file>: Define a custom search box based on a file containing the minimum and maximum cartesian values of each axis in angstrom.
# Usage
parKVFinder <.pdb> -B --custom_box <file>
parKVFinder <.pdb> --box --custom_box <file>The file must contain the minimum and maximum cartesian values of each axis in the following order: Xmin, Xmax, Ymin, Ymax, Zmin and Zmax. This file has a required format:
--------------------------------------------------------------------------------
Xmin Xmax Ymin Ymax Zmin Zmax
--------------------------------------------------------------------------------
Note: The values are separated by tab.
-
--residues_box <file>: Automatically set a search box based a file containing a tab-separated list of residues.
# Usage
parKVFinder <.pdb> -B --residues_box <file>
parKVFinder <.pdb> --box --residues_box <file>The file must contain a list of residues, in which we specify the residues as the residues number and chain identifier separated by an underscore character (_). This file has a required format:
--------------------------------------------------------------------------------
resnum1_chain resnum2_chain [...] resnumN_chain
--------------------------------------------------------------------------------
Note: The values are separated by tab.
-
--padding <real>: Define residues box padding. Adds a length in each box direction.
# Usage
parKVFinder <.pdb> -B --residues_box <file> --padding <real>
parKVFinder <.pdb> --box --residues_box <file> --padding <real>Default: 3.5.
-
-S <enum>or--surface <enum>: Define a surface representation. Options include: SAS and VdW. SAS specifies solvent accessible surface. VdW specifies van der Waals molecular surface.
# Usage
parKVFinder <.pdb> -S <enum>
parKVFinder <.pdb> --surface <enum>Default: VdW.
-
-L <.pdb>or--ligand <.pdb>: Define path to ligand PDB file.
# Usage
parKVFinder <.pdb> -L <.pdb>
parKVFinder <.pdb> --ligand <.pdb>-
--ligand_cutoff <real>: Define ligand radius distance cutoff.
# Usage
parKVFinder <.pdb> -L <.pdb> --ligand_cutoff <real>
parKVFinder <.pdb> --ligand <.pdb> --ligand_cutoff <real>Default: 5.0.
parKVFinder wiki
Getting started with parKVFinder