Refine Loops Panel

Summary

Refine the structure of loops in the protein that is displayed in the Workspace. The refinement can be run with periodic boundary conditions, in implicit solvent, and with an implicit membrane.

Opening the Refine Loops Panel

To open the Refine Loops panel, you can:

Using the Refine Loops Panel

To run a loop refinement:

  1. Display the structure to be refined in the Workspace.

  2. Choose a solvation model.

  3. Click one of the Find loops in Workspace structure buttons, which analyze the structure and load a list of loops into the loops table.

  4. Select the loops to be refined in the Run column of the table, and if necessary, change the starting and ending residue of the loop in the Res1 and Res2 columns. Loops are marked in the Workspace when you select the table rows.

  5. To select options and settings for the specified loop, click Options to open the Refine Loops - Options dialog box. This includes adding an implicit membrane and using crystal symmetry.

  6. To add constraints (pairwise, helical, spatial, or membrane), click Constraints and add the constraints in the panel that opens.

  7. Choose Job Settings from the Settings button menu,

    set the job parameters in the Job Settings dialog box, and click Run to run the job.

If you are refining a homology model, you should consider loops whose residues have a Homology Status of 2, meaning that their coordinates did not come from the template. These can be identified by labeling the Cα atom with this property. You can load these loops by clicking Non-Template.

If you want to refine more than one loop, you can run them one at a time, or you can select multiple loops in the table. When you select multiple loops, the loop refinement jobs are run sequentially. Any options that you set in the Refine Loops - Options dialog box apply to all loops. If you want to use different options for each loop, you should refine them one-at-a-time.

You can also refine two loops simultaneously. To do so, select two loops (and only two) in the Loops table and select Cooperative loop sampling in the Refine Loops - Options dialog box. The refinement alternates between the two loops until both are refined.

When a loop refinement begins, a validation program checks the loop features of the structure. Apparent errors are reported in a warning dialog box. You may choose Run All Features or Run Only Valid Features, but it is recommended that you make a note of the invalid features, click Cancel, and if appropriate correct the structure.

The time required to refine a loop scales approximately linearly with the length of the loop. It is recommended that extended sampling be used for loops longer than five residues, and ultra-extended sampling for loops longer than ten residues. You can do this in the Refine Loops - Options dialog box. This dialog box has many other options for loop refinement, including the following:

Refine Loops Panel Features

Solvation model option menu

Choose a continuum solvation model for the refinement. The choices are:

Find loops in Workspace structure buttons

Analyze the structure in the Workspace to locate loops, and load the Loops table with the results of the analysis. If you have a protein in the Workspace that came from homology modeling (Structure Prediction), you can click Non-Template to load only those loops that did not originate from the templates used for modeling. Otherwise, click All to load all loops.

Thess buttons are displayed when you select Refine loops from the Task menu.

Loops table

Displays a list of loops that can be selected for refinement. This table is displayed when you select Refine loops from the Task menu. The table has five columns:

Run Check boxes that can be used to select loops for refinement.
Feature Names of the loops. These names are generated automatically as loopn.
Chain Chain name
Res1 Residue number of the first residue in the loops. This value can be edited to change the length of the loop for refinement.
Res2 Residue number of the last residue in the loops. This value can be edited to change the length of the loop for refinement.

The table is initially empty. It is populated by clicking one of theFind loops in Workspace structure buttons. When you select a table row, the corresponding loop is highlighted in the Workspace.

Constraints button

Open the Refine Loops - Constraints dialog box, to set up distance, Cartesian, helical, spatial, and membrane constraints.

Options button

Open the Refine Loops - Options dialog box to set up options, including use of crystal symmetry, the solvent dielectric constant, the random seed for side-chain prediction, loop refinement method and other loop-related options.

Job toolbar

The Job toolbar is used to make settings for a job and to start it.

Job name text box

Enter a name for the job in this text box.

Settings button menu

This button opens the Job Settings dialog box. The arrow to the right opens a menu, from which you can make settings or perform actions that are related to the job.

The menu items are described below.

  • Job Settings—Make and save settings for the incorporation of the job into the Maestro project, the job name, the host, the distribution of subjobs, and any other application-specific job settings. Opens the Job Settings dialog box.
  • Preferences—Set general preferences for running jobs. Opens the Preferences panel at the Jobs - Starting section.
  • Write—Write the input files for the job but do not start it. The file names are based on the current job name, and the files are written to a subdirectory of the current working directory that is named with the job name.
Job status button

This icon indicates when there are jobs running for the application that belong to the current project. It starts spinning when the first job starts, and stops when there are no more jobs running. If a job fails to start, it changes to an exclamation point.

Clicking the button shows a small job status window that lists the job name and status for all active jobs submitted from the current panel (for Jaguar and MacroModel this means all jobs from any of the application panels). You can double-click on a row to open the Monitor panel and monitor the job, or click the Monitor button to open the Monitor panel and close the job status window. The job status is updated while the window is open. If a job finishes while the window is open, the job remains displayed but with the new status. The rows are colored according to the status: yellow for submitted, green for launched, running, or finished, red for incorporated, died, or killed. Click anywhere outside the window to close it.

Run button

Run the job with the current job settings.

Status bar

The status bar displays information about the current job settings for the panel. This includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. It also displays a message for a short time when you start a new job.

The status bar also contains the Help button, which opens the help topic for the panel.

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File: prime/refine_loops.html
Last updated: 14 Apr 2014