Real-Space Refinement Panel

Real-Space Refinement Panel Features

For each of the three real-space refinement tasks, a different set of controls is displayed in the center of the panel. These sets of controls are described in the section for each task.

• Grid spacing text box
• Set B-factors of atoms to be fit to option and text box
• Refine loops controls
• Predict side chains controls
• Minimize controls
• Calculation settings button
• Job toolbar
• Status bar

Grid spacing text box

Specify the grid spacing for the map used in the real-space refinement, in angstroms. For the Refine loops task, this text box is only available under the Manual option for the Build mode. The default is 0.5 for minimization and side-chain refinement, and depends on the mode for loop refinement.

Set B-factors of atoms to be fit to option and text box

This option allows you to set the B-factors for the atoms that are to be fit in the refinement process. You can enter a value in the text box. For the Refine loops task, this text box is only available under the Manual option for the Build mode. The default B-factor is 20 for minimization and side-chain refinement, and depends on the mode for loop refinement.

Refine loops controls

Loop refinements are done on a single loop, which can be chosen from theLoops table.

To run a loop refinement, the model sequence must match the reference sequence. If this is not the case, you should mutate the model first (see Mutate Model to Sequence Dialog Box).

Build mode options

These options set the grid spacing and the B-factors of the atoms to be refined:

• Automatic - resolution < 2.5Å—Select this option for automatic setting of the grid spacing and B-factors if the high-resolution limit is less than 2.5 Å. The grid spacing is set to 1.0 and the B-factor for the atoms to be fit is set to 5.0.

• Automatic - resolution > 2.5Å—Select this option for automatic setting of the grid spacing and B-factors if the high-resolution limit is greater than 2.5 Å. The grid spacing is set to 0.75 and the B-factor for the atoms to be fit is set to 45.0.

• Manual—Set the grid spacing and B-factors manually. The Grid spacing text box and Set B-factors of atoms to be fit to N Å option and text box become available when you select this option. Setting the B-factors to a low value improves the convergence of real-space refinements if the refined isotropic B-factors are high, which can happen if the B-factors of the atoms were refined when the coordinates contained substantial error.

Loops table

The Loops table lists all the loops, along with the starting and ending residue numbers. To choose a loop for refinement, select the table row. The chain name, and the starting and ending residue numbers are loaded into the Chain, Start, and End text boxes. The table columns are described below.

Feature	Loop label
Chain	Name of the chain in which the loop occurs.
Res1	First residue in loop.
Res2	Last residue in loop.

Chain, Start, and End text boxes

When you choose a table row, the chain name, and the starting and ending residue numbers are loaded into these text boxes. To change the limits of a loop, change the residue numbers in the Start and End text boxes.

Loops whose residues are missing from the structure are not listed in the table. To predict the structure of such a loop, you can select any loop and change the starting and ending residue numbers to span the loop you are interested in.

Load from Workspace

This button reloads the table from the Workspace structure, which is useful when the structure has been replaced or modified.

Bias to existing loop structure option

This option allows you to sample conformational space more heavily around the existing structure, with the result that the refined loop is more likely to resemble the input loop.

Predict side chains controls

The controls for the prediction of side chains consist of a set of standard picking controls, with which you can pick the residues whose side chains are to be refined.

If you open this panel from the Mutate Model to Sequence Dialog Box, the residues that were mutated are selected already, and you only need to start the job. If you have calculated a density fit (with the Density Fit Panel), you can select side chains for refinement by clicking in the Refine column for the desired residues, then clicking Refine Selected Sidechains to open this panel with the residues already selected. You can also select residues whose side-chain real-space R factor exceeds a certain threshold, by clicking Select and using the Atom tab of the Atom Selection Dialog Box.

Minimize controls

Real-space minimization performs a standard geometric variation of the coordinates to minimize the functional that includes both the force-field energy and the density fit.

If you have alternate conformations in your structure, you can only perform a minimization on one of the conformations at a time. Once you have minimized one, you can switch to the other and minimize it.

The controls for minimization consist of a set of standard picking controls, with which you can pick the residues to be refined. If you have calculated a density fit (with the Density Fit Panel), you can select residues whose density fit exceeds a certain threshold, by clicking Select and using the Atom tab of the Atom Selection Dialog Box.

Calculation settings button

This button opens the Calculation Settings Dialog Box, in which you can make a variety of settings.

Job toolbar

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

The Job Settings button opens the Real-Space Refinement - 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.