PrimeX Panel

This panel provides access to all the PrimeX functions in a dockable panel. In the process of refining a structure, you will use the tools in this panel multiple times, so it is useful to leave it open. By default it is docked into the Workspace, but you can undock it if you wish.

To open this panel, click the Tasks button and browse to Protein Preparation and Refinement → Protein X-Ray Refinement.

Using
Features
Additional Resources

Using the PrimeX Panel

Refinement of an X-ray structure usually involves many passes through different tasks. The PrimeX panel provides access to all those tasks, so you can easily go to the next task with a single click.

Toolbar

The toolbar provides access to tools for controlling the Workspace display.

	Surf Table Opens the Surface Manager Panel.
	+ Isovalue Increase the isovalue for the displayed surface (this makes the surface smaller). Each click on the surface increases the isovalue by 0.1 sigma. Using control-click increases the isovalue by 1.0 sigma.
	− Isovalue Decrease the isovalue for the displayed surface (this makes the surface larger). Each click on the surface decreases the isovalue by 0.1 sigma. Using control-click decreases the isovalue by 1.0 sigma.
	+ Extent Increase the extent of the density map that is displayed. Each click on the button increases the cube dimensions by the amount that has been selected from the button menu. Click the arrow to the right of the button to open this menu. The default value is 1 Å. The available values range from 0.5 Å to 16 Å, and are synchronized with the values on the − Extent button menu;.
	− Extent Decrease the extent of the density map that is displayed. Each click on the button decreases the cube dimensions by the amount that has been selected from the button menu. Click the arrow to the right of the button to open this menu. The default value is 1 Å. The available values range from 0.5 Å to 16 Å, and are synchronized with the values on the + Extent button menu.
	View Unit Cell Displays the unit cell boundaries in the Workspace.

Input Data button

Opens the Input Data Dialog Box so you can read structure and X-ray data into the project.

Checkpoint button

Save the contents of the Workspace as a new entry in the Project Table.

Export button

Opens a file chooser to export the final structure, and run a job to calculate R factors and add information to the file. Checking is done before the file chooser opens to ensure that the data is complete. The file is in Maestro format, which you can convert to PDB format using the pdbconvert utility. The log file for the export job contains information that you might want to add to the file.

Mutate Model to Sequence button

Opens the Mutate Model to Sequence Dialog Box so you can mutate the model to match the input sequence and perform side-chain refinement of the mutated model.

Reference Sequence button

Opens the Reference Sequence Panel so you can examine the reference sequence.

Optimize H-Bond Networks button

Opens the Interactive H-Bond Optimizer Panel to optimize H-bond networks and terminal amide and histidine orientations.

R-Factor Calculation button

Opens the R-Factor Calculation Panel to calculate R-factors for the structure.

Real-space refinement section

This section contains buttons that open panels for refinements that are performed in real space, with a weighting of the OPLS force field and the X-ray terms to drive the refinements.

Refine Loops button: Opens the Real-Space Refinement Panel with tools for refining loop conformations.
Predict Side Chains button: Opens the Real-Space Refinement Panel with tools for predicting side-chain conformations.
Minimize button: Opens the Real-Space Refinement Panel with tools for coordinate minmization.
Ligand/Solvent Placement button: Opens the Ligand/Solvent Placement Panel, so you can place a ligand or solvent molecules in a region that contains an appropriate amount of density.
Water Placement button: Opens the Water Placement Panel so you can place waters in regions that contain an appropriate amount of density.

Reciprocal-space refinement section

This section contains buttons that open panels for reciprocal space refinement of coordinates or B-factors.

Minimization button: Opens the Reciprocal-Space Refinement Panel for minimization of coordinates or B-factors.
Rigid Bodies button: Opens the Reciprocal-Space Refinement Panel to perform rigid-body minmization of parts or all of the model.
Simulated Annealing button: Opens the Reciprocal-Space Refinement Panel to run a simulated annealing calculation.

Map-related section

This section contains buttons for creating or using maps.

Create Map button: Opens the Create Map Panel, so you can set up and create a density map, difference map, or omit map.
Density Fit button: Opens the Density Fit Panel to display a per-residue assesment of how well the electron density from the current model fits the electron density map.
Density Blobs button: Opens the Density Blobs Panel, which displays a list of unaccounted density regions based on the Fo-Fc map in the Workspace.

PrimeX Panel

Using the PrimeX Panel

PrimeX Panel Features

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