Receptor Grid Generation Panel

• Grid Site and Extent
• Receptor-based Constraints
• Rotatable Groups
• Excluded Volumes

Grid Site and Extent

Glide uses two “boxes” to organize the docking process:

• The grids themselves are calculated in the space defined by the enclosing box, or grid box or outer box. This is also the box within which all the ligand atoms must be contained.

  The center of this box is displayed in the Workspace as a set of coordinate axes colored bright green, and the boundaries of the box as a purple wire frame cube. In any docking job using these receptor grids, ligands are confined to the enclosing box.

• During the site point search, the ligand center is allowed to move within the ligand diameter midpoint box, or inner box. This box gives a truer measure of the effective size of the search space. However, ligands can move outside this box during grid minimization.

The only requirement on the grid box is that it is big enough to contain all ligand atoms when the ligand center is placed at an edge or vertex of the inner box. Grid boxes that are larger than this are not useful: they take up more space on disk and in memory for the scoring grids, which take longer to compute. The maximum side size of the grid box is 80 Å.

The ligand center is defined in a rigid-docking run as the midpoint of the line drawn between the two most widely separated atoms. The definition changes slightly for flexible docking, where the ligand center becomes the midpoint between the two most widely separated atoms of the core region—the part of the ligand remaining after each of the end-groups has been stripped off at the terminal end of the connecting rotatable bond.

The two boxes share a common center. Thus, the operations that center one box also center the other. Information on the two boxes is written to the Maestro file for the receptor.

Each rigidly docked ligand or flexibly docked conformation has an associated length, L, which can be defined as twice the distance from the ligand center to its farthest atom. The required relationship between L and the lengths E and B of the outer and inner boxes for successful placement of the ligand center anywhere within the inner box is:

E ≥ B + L

The grid box must be large enough in each dimension to hold the length of the inner box plus the maximum length of any ligand. If a larger ligand is encountered, not all positions for the center of the ligand in the inner box are accessible. The effective inner box for that ligand will be smaller than the dimension nominally specified. In any docking job using these receptor grids, ligands are confined to the grid box.

Receptor-based Constraints

Glide constraints are receptor-ligand interactions that you believe to be important to the binding mode. Up to ten constraints can be defined in a grid generation job. When you run Glide docking jobs, you can select as required interactions a subset of the constraints defined in the receptor grids, up to a limit of four. By setting such requirements, you can often significantly enrich the final results and speed up docking, as Glide is able to discard ligands, conformations, or poses that do not meet these criteria early on in their evaluation for docking suitability.

There are five types of constraints available: positional constraints, NOE constraints, H-bond constraints, metal constraints, metal coordination constraints. Two other types, core constraints and torsional constraints, only depend on the ligand and are specified during docking setup (see Ligand Docking Panel DEPRECATED).

• A positional constraint defines a spherical region that must contain a particular kind of ligand atom. The specific kind of atom is defined during docking setup, using SMARTS patterns. This is a maximum distance constraint, and is the most general kind of constraint. Positional constraints allow you to require interactions between any kind of receptor and ligand atoms, while at the same time placing tighter restrictions on the ligand atom position than is typical with other constraint types. The spherical region does not have to be centered on an atom—it can be anywhere, such as where a ligand atom might be expected to lie.

  For example, a hydrogen-bond acceptor in the receptor might be capable of forming hydrogen bonds in two directions, but only one of these results in good binding. While setting an H-bond constraint allows a ligand hydrogen atom to lie in either of these directions, a positional constraint can require it to be in the “good” direction. The constraint could be set by selecting a hydrogen atom on a ligand that bonds in the “good” direction to define the position of the constraint. For this purpose, it is helpful to display a typical ligand in the Workspace to aid in selecting appropriate positions for the constraints.

• A NOE (nuclear Overhauser effect) constraint is similar to a positional constraint, requiring that ligand atoms lie between two spheres centered at a particular position. It only differs from a positional constraint in having a smaller sphere from which the ligand atoms are excluded. This is a constraint to a distance range.

• An H-bond constraint is a requirement that a particular receptor-ligand hydrogen bond be formed.

  For hydrogen-bonding interactions, the receptor atom must be a polar hydrogen (including thiol H in cysteine), nitrogen, or oxygen. If you choose an atom with one or more symmetry-equivalent atoms in its functional group, the symmetry-equivalent atoms are all selected as well by default, and collectively count as one constraint. For example, if you create a constraint by picking one oxygen atom of a carboxylate group, Glide includes the other oxygen atom in the same constraint. A ligand interaction with either oxygen atom satisfies that single constraint. However, you can turn off the use of symmetry so that only the chosen atom is used.

  The receptor atoms selected must also be close enough to the ligand that satisfying the constraints is possible. You do not need to specify limits on distances or angles between receptor and ligand atoms for the constraint: Glide sets these values internally, to H-acceptor distances of 1.2 to 2.5 Å; donor angles greater than 90°, and acceptor angles greater than 60°. These values are looser than those employed by Maestro for displaying H-bonds. The receptor atoms selected for constraints must be inside the grid box (which is displayed in purple) or within bonding range of it.

• A metal constraint is a requirement that a particular metal-ligand interaction is present when the ligand is docked. The ligand atom must lie in a sphere around a specified receptor metal atom, and therefore the constraint on the ligand atom has no directionality. For metal constraints the ligand-metal distance must be no greater than the sum of the van der Waals radii of the metal and ligand atoms plus 0.4 Å.

• A metal coordination constraint is a requirement that a ligand atom lie within a given distance of an optimal coordination site for a metal atom. It differs from a metal constraint in that the constraint sphere is centered on a potential ligand coordinating atom rather than on the metal, and is thus directional.

  Metal coordination constraints require a ligand atom to lie within a specified distance of a coordination site, which is the location that a ligand atom should occupy for optimal bonding with the metal. For each metal, the possible coordination sites are identified, and a constraint sphere is placed at the ideal location of a ligand donor atom at the available site. This differs from the metal constraint feature, in which a constraint sphere is placed on the metal. The metal coordination constraint has directionality, whereas the metal constraint has none. You can choose to use any or none of the sites found for a given metal.

When constraints setup is complete and the grid generation job is run, Glide writes a file containing the information about the constraints. Subsequent docking jobs use this file to determine whether a given ligand pose satisfies the constraints. If the base name for writing grid files is gridbase, the constraints file is named gridbase.cons. Not all of these constraints are used in a given docking job: when you set up the docking job, you can choose which constraints to apply.

Rotatable Groups

You can choose to treat receptor hydroxyl and thiol groups as rotatable (flexible) rather than rigid, and select the groups that are actually treated as rotatable. H atoms in flexible receptor groups cannot be used for constraints.

The hydroxyl groups in residues such as Ser, Thr, and Tyr and the thiol group in Cys can adopt different orientations with different ligands. Glide can allow such groups to adopt different orientations when ligands are docked, to produce the most favorable interaction. For Ser and Thr, the hydroxyls can be oriented in any of the three local minima, and likewise for the thiol of Cys; for Tyr, they can be in either of the two local minima.

Treating hydroxyl and thiol groups as rotatable takes more time in the docking run, but the extra time is much less than that taken by generating grids for each combination of flexible group orientations and docking to each of these grids.

For example, with 4 flexible groups, an SP docking run takes about twice as long as a run with no flexible groups. If each of these groups can take two possible orientations, there are 16 combinations. To dock to all of these combinations without allowing flexibility would therefore require 16 grid calculations and 16 non-flexible docking runs, and the results from the individual runs would have to be collated at the end.

Note: Once you have set up a grid with flexible groups, the flexibility is used in docking, and cannot be turned off.

Excluded Volumes

In some situations, you might want to prevent ligands from occupying certain regions of space. For example, if you have a pocket near the active site where ligands are known not to bind, you might want to stop ligands from occupying that pocket. Another situation is searching for ligands that might be immune to drug-resistant mutations, to check the alignment by ensuring that the drug only occupies the space that is occupied by the substrate. A third case is where parts of a protein are missing, and you want to prevent the ligand from occupying that region.

You can prevent ligands from occupying regions of space by defining excluded volumes in those regions. You would not normally need to place spheres on regions occupied by the protein, because these are already excluded in the docking process (due to the potentials).

Phase also allows you to define excluded volumes for a pharmacophore hypothesis. You can import a Phase excluded volume file (.xvol) to use with a Glide grid, by clicking Import and navigating to the file. Importing Phase excluded volumes is only likely to be useful if the ligand you are using as the reference ligand for Glide is the same as that used for the Phase hypothesis, or at least has pharmacophore features that superimpose well on the Glide ligand. To check the alignment, you should include both the Phase hypothesis with its reference ligand and the Glide native ligand in the Workspace.

Glide excluded volume files (.gxvol) cannot be used with Phase, however, because the format is not compatible, and they contain information other than the sphere coordinates and radii.

Receptor Grid Generation Panel Features

• Receptor tab
• Site tab
• Constraints tab
• Rotatable Groups tab
• Excluded Volumes tab
• Job toolbar
• Status bar

• Receptor
• Site
• Constraints
• Rotatable Groups
• Excluded Volumes

Receptor Tab Features

• Define receptor section
  • Pick to identify ligand option and menu
  • Show markers option
• Van der Waals radius scaling section
  • Scaling factor text box
  • Partial charge cutoff text box
• Use input partial charges option
• Generate grid suitable for peptide docking option
• Advanced Settings button

Define receptor section

This section contains options for defining the part of the system in the Workspace to be treated as the receptor. If only the receptor is included in the Workspace, you can ignore these options.

If the structure in the Workspace is a receptor with a ligand or a SiteMap binding site, use these options to pick the ligand molecule or the site. The ligand or the site will be excluded from receptor grid generation. Everything not defined as the "ligand" is treated as part of the receptor.

Pick to identify ligand option and menu

If the structure contains a ligand or a SiteMap site as well as a receptor, ensure that this option is selected. If the ligand is a molecule within the ligand/receptor complex entry, choose Molecule from the menu. If the ligand is a separate entry, or if you are using the results of a SiteMap calculation to define the binding site, choose Entry from the menu. Then pick an atom in the ligand molecule or one of the site points. The ligand or site is now distinguished from the receptor.

Show markers

If this option is selected, when the ligand molecule is picked it is marked with green markers. Deselect the option to remove the markers.

Van der Waals radius scaling section

Glide does not allow for flexible receptor docking (apart from hydroxyl rotations). However, scaling of van der Waals radii of nonpolar atoms, which decreases penalties for close contacts, can be used to model a slight "give" in the receptor and the ligand. (Receptor flexibility can be modeled with Glide/Prime Induced Fit docking—see Induced Fit Docking).

You can use the features under Van der Waals radii scaling to scale the van der Waals radii of those receptor atoms defined as nonpolar by a partial charge threshold you can set. For ordinary Glide docking, it is recommended that receptor radii be left unchanged, and any scaling be carried out on ligand atoms. Receptor scaling is probably most useful when the active site is tight and encapsulated. information on scaling of vdW radii of nonpolar ligand atoms, see the Ligand Docking Panel topic.

Scaling factor text box

This text box specifies the scaling factor: van der Waals radii of nonpolar receptor atoms are multiplied by this value. The default value is 1.00, which means that the receptor atom radii are not scaled.

Partial charge cutoff text box

Scaling of vdW radii is performed only on nonpolar atoms, defined as those for which the absolute value of the partial atomic charge is less than or equal to the number in the text box. Since this is an absolute value, the number entered must be positive. The default for receptor atoms is 0.25.

Use input partial charges option

Select the Use input partial charges option to use partial charges from the input structures instead of those from the force field. This option is useful if, for example, you have obtained improved partial charges around the active site, such as those from a QSite calculation or a QM-Polarized Ligand Docking calculation.

Generate grid suitable for peptide docking option

If you want to dock peptides with Glide, select this option to generate grids that are set up for peptide docking. A grid that is prepared for peptides can only be used in the SP-peptide docking mode. (You can dock ligands other than peptides with these grids: no restriction to peptides is applied.)

Advanced Settings button

To perform scaling of van der Waals radii on a per-atom level, or to allow aromatic hydrogen and halogen bonds to be considered, click this button, and make the settings in the Receptor - Advanced Settings dialog box.

Site Tab Features

• Display box option
• Center options
  Centroid of Workspace ligand (selected in the Receptor tab)
  Centroid of selected residues
  Supplied X, Y, Z coordinates
• Size options
  • Dock ligands similar in size to the Workspace ligand option
  • Dock ligands with length <= option, slider and text box
• Advanced Settings button

Display box option

This option is selected by default, so that the purple enclosing box outline and the green axes at the center are displayed when you enter the tab. Deselect this option to undisplay the box and its center.

Center options

Select one of the options under Center to determine how the center of the scoring grid is defined:

Centroid of Workspace ligand (selected in the Receptor tab)

Center grids at the centroid of the ligand molecule that was selected in the Receptor tab. This ligand should be in the Workspace. If such a ligand has been selected, this option is the default. The Advanced Settings button is available with this option.

Centroid of selected residues

Center grids at the centroid of a set of residues that you select. With this option you can define the active site (where grids should be centered) with only the receptor in the Workspace. You might want to do this if the Workspace includes a SiteMap binding site, as the centroid of the site might not be in the optimal location, and particularly so if the site is not well defined or the site points extend over a broad region.

The Specify Residues button opens the Active Site Residues Dialog Box, in which you can pick the residues that best define the active site.

The Specify Residues button is only available when you choose this option; the Advanced Settings button is not available with this option.

Supplied X, Y, Z coordinates

Center grids at the specified coordinates.

Center the grid at the Cartesian coordinates that you specify in the X, Y, and Z text boxes. The coordinates of the grid center chosen by any of the other two methods are displayed in these text boxes. These text boxes are only available when you choose this option. The Advanced Settings button is available with this option.

Size options

These options specify the size of the grids, which must be larger than the ligands to be docked.

 

Dock ligands similar in size to the Workspace ligand option

Select this option if the ligands to be docked are of the same size as, or smaller than, the Workspace ligand. This is the default option if you choose Centroid of Workspace ligand for the Center option. Glide uses the position and size of the ligand to calculate a default center and a default size for the grid box.

If the Workspace includes a SiteMap binding site, you might want to reduce the size of the grid box, because it is likely that the site is larger than defined by a ligand. You might also want to specify the center of the box by selection of a few residues from the receptor, as the centroid of the site might not be in the optimal location. This is particularly so if the site is not well defined or the site points extend over a broad region.

Dock ligands with length <= option, slider and text box

Specify the maximum size of the ligands to dock, by adjusting the slider or entering the value in the text box. This is the default option if you choose Centroid of selected residues or Supplied X, Y, Z coordinates for the Center option. The slider is set to 20 Å by default.

Advanced Settings button

Click this button to change the size of the inner grid box, or ligand diameter midpoint box. The diameter midpoint of a ligand is the midpoint of the longest line segment that can be constructed between any two atoms in the ligand. The diameter midpoint of each docked ligand remains within this box in the site-point search stage, but can move outside this box in the grid minimization stage (see Figure 2 in Glide Methodology).

When you click this button, the Site - Advanced Settings dialog box opens, and the inner is displayed as a cube outlined in bright green. You can use the Size sliders to increase or decrease the dimensions of each side of the box. The default is 10 Å on each side; the allowed range is 6 Å to 14 Å. When you adjust the sliders, the enclosing box also changes size, to keep the distance between the faces of the enclosing box and the inner box the same.

A larger inner box can be useful to allow ligands to find unusual or asymmetric binding modes in the active site. Conversely, if the default inner box allows ligands to stray into regions you know to be unfruitful, you can confine their midpoints to a smaller box, eliminating some of the less useful poses and saving calculation time. Changing the shape of the box can be useful when the active site is spatially extended in one or more directions.

Constraints Tab Features

• Defined constraints counter
• Tabs

Defined Constraints Counter

The total number of constraints that have been defined so far is displayed at the top of the tab:

N constraints have been defined (limit is 10 total)

The number N is the sum of the numbers of positional or NOE, H-bond/metal, and metal coordination constraints. These numbers are displayed in parentheses in the tabs of each subtab.

Tabs

• Positional/NOE
• H-bond/Metal
• Metal Coordination

This subtab provides tools for defining positional and NOE (nuclear Overhauser effect) constraints. Positional constraints are defined as spheres that specified atoms of the ligands must occupy. NOE constraints are similarly defined as spherical shells (the region between two spheres) that specified atoms of the ligands must occupy.

• Positions table
• New button
• Delete and Delete All buttons
• Show markers option
• Label positions option

Positions table

This table displays the positional constraints you have chosen, giving the name and coordinates of the sphere center. For positional constraints a maximum distance is shown, which is the radius of the constraint sphere; for NOE constraints a minimum and a maximum distance are shown. The coordinates and the radius are given in angstroms. You can select a single constraint in the table, and edit the coordinates and radii of the spheres by clicking in the table cell and changing the value, or delete the constraint by clicking the Delete button. If you want to convert a positional constraint to an NOE constraint, you can do so by providing a minimum distance.

New button

To add a positional constraint or an NOE constraint, click the New button. This button opens the New position/NOE dialog box, in which you can pick atoms with the standard picking controls to define the centroid of the constraint; name the constraint; select the constraint type (Position or NOE); specify the radius for a positional constraint, or the minimum and maximum distance for an NOE constraint. The position is the centroid of the selected atoms, and must be inside the enclosing box. While picking is in progress, the constraint is marked with a gray sphere. For NOE constraints, both spheres are displayed. When you click OK, the constraint is added to the table if it is inside the enclosing box; otherwise a warning is displayed.

Delete and Delete All buttons

To delete a single constraint, select it in the table and click Delete. To delete all the listed constraints, click Delete All.

Show markers option

This option is selected by default. The selected constraint is marked by one or two yellow spheres, depending on the constraint type. The other positional or NOE constraints are marked by red spheres. Deselect this option to remove the markers.

Label positions option

This option is selected by default. If Show markers is selected, this option displays the name of the constraint in the Workspace. The labels are colored the same as the constraints. Deselect this option to remove the labels.

The H-bond/Metal subtab contains controls for setting up hydrogen-bonding or metal constraints. These constraints are made to individual atoms, which can be picked in the Workspace.

Up to ten symmetry-distinct receptor atoms can be chosen as possible H-bond or metal constraint sites. The H atoms in flexible receptor groups cannot be used for constraints.

• Receptor atoms table
• Pick atoms option
• Delete and Delete All buttons
• Show markers option
• Label atoms option

Receptor atoms table

As you select atoms in the receptor, they appear in this table. Each constraint is identified by a name and an atom specification. A default constraint name is supplied. You can change the name by editing the table cell. The atom specification is given in the following format:

atom_number:chain: residue_name residue_number : atom_name : symmetry_set

where

• atom_number = Maestro atom number
• chain = chain name
• residue_number = residue number + insertion code
• atom_name = PDB atom name
• symmetry_set = atom name or symmetry-equivalent atom set

For example:

341:C:ASN 239 : OD1: OD1

If the picked atom is part of a symmetry-equivalent set, its identification is followed by square brackets enclosing the number and name of each atom in the set, separated by commas:

2203:C:GLU 192 : OE2:[2203: OE2,2202: OE1]

The default constraint name is chain:residue_name:residue_number:atom_name(type) where the quantities except type are defined above, and type is either hbond or metal, for example,

C:ASN:239:OD1(hbond)

The Use Symmetry column indicates whether symmetry-equivalent atoms are included with the picked atom for a constraint or not. Symmetry can be turned on or off by selecting or clearing the check box in this column. If you clear the check box, only the atom that you pick is used for the constraint, and the symmetry information is removed from the Atom column. Symmetry is on by default.

Pick atoms option

When this option is selected, you can define H-bond/metal constraints by picking appropriate atoms in the receptor, which must be displayed in the Workspace. To define hydrogen bonds, pick any polar H, N, or O atom in the receptor. (The atom is identified in the status bar when the pointer is over the atom, as described in Status Bar.) Glide automatically identifies symmetry-equivalent atoms as well, for example the other oxygen in a carboxylate group. The symmetry can be turned on or off in the Use Symmetry column. If it is on, any one of the symmetry-equivalent atoms will satisfy the constraint. If it is off, the atom that you picked is used for the constraint. To define metal sites, pick the metal atom.

Delete and Delete All buttons

To delete a single constraint, select it in the table and click Delete. To delete all the listed constraints, click Delete All.

Show markers option

This option is selected by default. A cross and padlock appear next to each atom picked, colored light blue for the selected constraint (the last one picked), and red for unselected constraints. If the picked atom is one of a set of symmetry-equivalent atoms, all the atoms in the set are marked. Deselect this option to remove the markers.

Label atoms option

This option is selected by default. If Show markers is selected, this option displays the name of the constraint in the Workspace. The labels are colored the same as the constraints. Deselect this option to remove the labels.

This subtab provides tools for defining constraints to possible coordination sites of a metal atom. For each metal atom, the available coordination sites are identified, based on the coordination of the metal to the receptor. A constraint sphere is placed at the ideal location of a ligand donor atom at the available site. This differs from the metal constraint feature, in which a constraint sphere is placed on the metal. The metal coordination constraint has directionality with respect to the metal, whereas the metal constraint has none. You can choose to use any or none of the sites found for a given metal.

• Receptor metal atoms table
• Pick metal atoms option
• Rotate option
• Show markers option
• Label regions option
• Delete and Delete All buttons

Receptor metal atoms table

This table displays the metal coordination constraints you have chosen, giving a name for the set of coordination sites associated with the metal, the coordinates of the ideal coordination sites, and the maximum distance of a constrained ligand atom from that site. You can edit the constraint name, the coordinates and the radii of the spheres by clicking in the appropriate table cell and changing the value.

When you select a row in the table, the rows for all the other sites associated with the metal atom are also selected, and the spheres are highlighted in the Workspace in red. Any other spheres are colored gray.

Each table row has a column of check boxes that you can select or deselect to use or ignore each site. When you clear one of the check boxes, to ignore the site, the sphere in the Workspace is colored gray and made more transparent.

To delete the set of sites for a given metal, select a table row for the metal and click Delete. You cannot delete individual sites: instead, you should clear the Use check box to remove them from consideration.

Pick metal atoms

Pick receptor metal atoms in the Workspace to define metal coordination constraints. The atom is identified in the status bar when the pointer is over the atom, as described in Status Bar. It is also highlighted, if predictive highlighting is enabled.

When a metal is picked, the possible coordination sites are identified and rows are added to the Receptor metal atoms table with the coordinates of the sphere and the maximum distance. Each of the possible coordination constraints is shown in the Workspace as a sphere centered at the coordination site, with the radius equal to the maximum distance. If there is more than one possible coordination geometry, all geometries are listed.

Rotate

Rotate the set of coordination sites around the metal center, with the usual actions for Workspace rotation. As coordination orientations can vary considerably in a complex structure such as a protein, it may be necessary to to adjust the orientations of the sites from their initial locations, so that the constraint spheres cover the desired regions of space.

Show markers option

This option is selected by default. The selected set of coordination sites are marked with red spheres, and the other sets are marked with yellow spheres. Deselect this option to remove the markers.

Label regions option

This option is selected by default. If Show markers is selected, this option displays the name of the corresponding coordination site set (the constraint name) in the Workspace on each sphere. Deselect this option to hide the labels.

Delete and Delete All buttons

To delete a single set of coordination sites, select one of the sites in the table and click the Delete button. To delete all the listed constraints, click the Delete All button.

Rotatable Groups Tab Features

• Available groups table
• Deselect All button
• Pick groups option

Available groups table

This table lists the available rotatable groups, which are all rotatable groups in the grid box. The group is identified by the hydrogen atom number, the chain name, residue name and residue number. You can select a group for use as a rotatable group by clicking in the Allow rotation column. When you do so, the rotatable group is marked in the Workspace, and the check box in the column is checked. Clicking again deselects the group and clears the check box.

The check boxes are unchecked by default, unless you read in a receptor from a previous grid generation for which rotatable groups were defined, when the boxes you checked for that receptor in the previous run are checked.

Deselect All button

Click this button to clear the selection of rotatable groups. All check boxes in the Allow rotation column of the table are cleared. This provides a quick way of turning off rotatable groups.

Pick groups option

Pick the hydrogen atom in a hydroxyl or thiol group to select or deselect it for use. The rotatable group is marked in the Workspace, and the group is checked in the Use column of the Available groups table.

Excluded Volumes Tab Features

• Excluded volumes table
• New button
• Import button
• Delete and Delete All buttons
• Show markers option
• Label excluded volumes option

Excluded volumes table

This table lists each sphere, with its name, the coordinates of its center, and its radius. You can select multiple rows in the table to delete. All the table cells are editable, so you can change the characteristics of the excluded volume after adding it to the table.

New button

Click this button to add a new excluded volume sphere. The New Excluded Volume dialog box opens, so you can define the sphere center and radius and provide a name. The sphere center is placed at the centroid of the atoms that you pick in the Workspace (e.g. atoms on either side of a pocket you want to exclude).

Import button

Import excluded volumes from a Phase hypothesis. Only the sphere center and sphere radius are imported. Opens a dialog box, in which you can navigate to the desired .xvol file.

Note: You must ensure that the hypothesis is in the same frame of reference as the receptor. No translation or rotation of the coordinate frame is done when the excluded volumes are imported.

You can check the alignment by including in the Workspace the native ligand for the receptor and the reference ligand for the hypothesis, to see if they are properly superimposed. If there is no reference ligand for the hypothesis, include the hypothesis in the Workspace and ensure that the sites in the hypothesis are placed at appropriate locations on the native ligand. If you don't see a reasonable alignment, the excluded volumes are likely to be of little value.

Delete and Delete All buttons

Select table rows and click Delete to delete the selected volumes. Click Delete All to delete all the excluded volumes.

Show markers option

Select this option to display the excluded volume spheres in the Workspace. The selected volumes are colored red; the unselected volumes are colored yellow.

Label excluded volumes option

Label the excluded volumes in the Workspace with the names listed in the table.

 

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Receptor Grid Generation - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Related Topics

• Ligand Docking Panel DEPRECATED
• Glide Overview
• Receptor Grid Generation - Job Settings Dialog Box