Prime Macrocycle Sampling Panel

Sample the conformations of a ligand-sized structure that contains macrocycles.

To open this panel, click the Tasks button and browse to General Modeling → Macrocycle Sampling.

  • Using
  • Features
  • Additional Resources

Using the Prime Macrocycle Sampling Panel

The sampling algorithm takes the macrocycle backbone and splits it into two pieces, which are independently sampled, making use of libraries of known angles. The halves are reconnected if they match, and the backbone structures are clustered. The chains attached to the macrocycles are rebuilt and the structure is minimized. The relative energy of the generated macrocycle conformations is returned as a Maestro property, model dPrime Energy.

Structures with multiple macrocycles that are not directly connected should not be sampled, as only one of the macrocycles is processed. Very large macrocycles (more than 40 atoms in the ring) should also be avoided.

You can use multiple processors to run the job, as the master job can distribute the job both over input structures and sampling cycles.

If you want to run the job from the command line, you can choose Write from the Job Settings (gear) button menu, and write out the shell script and Maestro file needed to run the job, in a subdirectory named with the job name.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see macrocycle_sample.py Command Help.

Prime Macrocycle Sampling Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Sampling intensity options

Specify the amount of sampling done to generate conformations.

  • Fast—Run the sampling algorithm once, generating up to 100 conformations per input structure.

  • Thorough—Run the sampling algorithm 10 times with different split points, generating up to 1000 conformations per input structure. These 10 runs can be distributed over multiple processors.

  • Custom—Generate up to the number of conformations per input structure specified in the text box. If the number specified is less than 100, only one sampling run is done; if it is 100 or more, 10 runs are done, as for thorough sampling. These 10 runs can be distributed over multiple processors.

Sample peptide bonds option

Sample rotations around peptide bonds. These are kept fixed (planar) by default. The increased conformational space approximately doubles the calculation time for each peptide bond sampled.

Preserve major ring shape option

Preserve the shape of the ring itself by applying curvature restraints during sampling. This produces conformations of the ring atoms that are similar to the input ring while allowing full sampling flexibility for the rest of the structure.

Job toolbar

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

The Job Settings button opens the Prime Macrocycle Sampling - 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.

Tutorials