Create Shape Data File Panel

Create a data file from a set of ligands that can be used for shape-based screening on a GPU. This file is analogous to a Phase database for screening on a CPU.

To open this panel: click the Tasks button and browse to Ligand-Based Virtual Screening → Create Shape Data File (For GPU).

  • Features
  • Additional Resources

Create Shape Data File Panel Features

Ligands section

Specify the ligands to be used to create the shape data file. The preparation neutralizes the structure and keeps the lowest-energy stereoisomer; it does not vary the tautomerization.

Use ligands from option menu

Choose the structure source for the current task.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
  • Phase Database (local)—Use the structures in the specified local Phase database. When this option is selected, the Local database text box and Browse button are displayed.
  • Phase Database (remote)—Use the structures in the specified remote Phase database. When this option is selected, the Remote database path text box is displayed. Enter the full path to the database on the remote host in the text box.
Input structure file text box and Browse button

Enter the file names in this text box, or click Browse and navigate to the files. The names of the files you selected is displayed in the text box. The allowed file types are: Maestro.

Local database text box and Browse button

If you chose Phase database (local) from the Use ligands from option menu, enter the path to the database in this text box, or click Browse and navigate to the database. The database path is displayed in the text box.

Remote database path text box

If you chose Phase database (local) from the Use ligands from option menu, enter the full path to the database on the remote host in the text box.

Run ligand preparation option

Run a ligand preparation with LigPrep.

This option is disabled if you select Identify unique ligands by, or if the input ligands come from a Phase database, as it is assumed that the ligands are already prepared.

Conformers section

Make settings for the generation or perception of conformers in the ligand source.

Identify unique ligands by option and menu

Choose the criterion used to associate structures that originate from the same ligand. The structures that belong to the same ligand have the same composition and connectivity, but may be conformers, tautomers, ionization states, or stereoisomers. These options allow you to decide which structures are considered to be an instance of a unique ligand.

This feature is not available if you select Run ligand preparation, as the ligand preparation labels the structures that are derived from each input ligand. If it is selected, the Generate ligand conformers options are not available, as it is assumed that the conformers have already been generated.

  • Stereoisomers—use stereochemistry in addition to connectivity and composition to identify structures that belong to the same ligand. Stereoisomers are considered to belong to different ligands.
  • Connectivity—use connectivity and composition, but not stereochemistry, to identify structures that belong to the same ligand. Stereoisomers are considered to belong to the same ligand.
  • Property—use a selected Maestro property to define which structures belong to the same ligand. The Property name option menu is displayed, so you can select the property. The most commonly used property is the title, which often is an identifier for the ligand.
Property name option menu

Select the property to be used to associate structures that originate from the same ligand. The property names are taken from the first structure in the file, so you should ensure that the property you choose exists for each structure in the file, not just the first.

Generate ligand conformers options

Select this option to generate ligand conformers with ConfGen, and choose an option for coverage (Rapid or Thorough). The conformers are ordered by rank.

If you deselect this option, it is assumed that the input structure file contains conformers, grouped together in the file. If you select Identify unique ligands by, this option is disabled, as it is assumed that the conformers have already been generated.

Minimize output conformers option

Minimize the energy of each output conformer. This produces better structures (minimum on the potential energy surface), but takes substantially more time than the conformer generation. The conformers are ordered by energy.

Shape Data File section

Make settings for the information that is stored in the shape data file.

Shape type options

Select the type of shape to create.

  • Typed pharmacophore—Treat each structure as a collection of pharmacophore sites, whose locations are assigned by applying Phase pharmacophore feature definitions. Overlapping volumes are computed only between sites of the same feature type. Each site is represented by a sphere of radius 2 Å.
  • Typed atoms—Treat each structure as a collection of atoms, whose volumes are defined by their van der Waals radii. Overlapping volumes are computed only between atoms of the same type. The MacroModel atom typing scheme is used—see MacroModel Atom Types for information.
  • Untyped atoms—Treat each structure as a collection of atoms, whose volumes are defined by their van der Waals radii. Overlapping volumes are not restricted by atom type.
Store shapes of no more than the first N conformers text box

Store shapes in the data file for only the first N conformers. The conformers are ordered by energy, if the energies were minimized, otherwise they are ordered by rank metrics calculated during conformer generation.

Job toolbar

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

The Job Settings button opens the Create Shape Data File - 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. It also displays a progress bar for the job.

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.

Tutorials

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