Refine Loops Panel

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.

For technical details about loop refinement, see Loop Refinement Technical Details.

To open this panel: click the Tasks button and browse to Protein Preparation and Refinement → Refine Loops.
To open this panel from the entry group for the results of a homology modeling job, use the Workflow Action Menu .

  • Using
  • Features
  • Additional Resources

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. Choose a force field.

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

  5. 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.

  6. 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.

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

  8. 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:

  • Cooperative sampling of two loops
  • Return of multiple loop structures for a single loop
  • Distributed processing of loop refinement
  • Adjustment of side chains near the loop
  • CA atom restraint
  • Use of crystal symmetry
  • Use of implicit membrane
  • Atom overlap

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 prime Command Help and prime—Build and Refine Protein Structures.

Refine Loops Panel Features

Solvation model option menu

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

  • VSGB—Use the variable-dielectric generalized Born model, which incorporates residue-dependent effects. The solvent is water.
  • Vacuum—Do not include solvation.
  • Chloroform—Use chloroform as the solvent, modeled with the Surface Generalized Born (SGB) method.
Force field option menu

Choose the force field for the current task. The choices are OPLS_2005 and OPLS4. The default is OPLS4 if it is available, otherwise it is OPLS_2005, unless you set the default in the Force Field settings section of the Preferences Panel.

Use customized version option

Use your customized version of the OPLS4 force field, rather than the standard version in the distribution. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license.

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 the Find 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

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

The Job Settings button opens the Refine Loops - 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