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Density Fit Panel |
This panel displays a measure for each residue of how well the electron density predicted by the current structure fits the current electron density map.
To open the Density Fit panel, you can:
Click Density Fit in the PrimeX panel.
This panel can be used to identify residues that should be targeted for further refinement, based on the fit to the electron density map. The values displayed are a measure of the relative error in the density. Side chains can be selected for refinement.
Each of the three fits (total, backbone and side chain) are stored as atom-level properties with the structure, and can be used in the Atom tab of the Atom Selection dialog box to select atoms for refinement. Since each atom in a residue has the same value of the property, setting the numeric threshold selects all atoms in residues with the property value greater than the threshold.
Table of real-space R factors. Each row contains the data for a single residue. You can select a single row in the table, and the Workspace view zooms in to the selected residue. You can sort the table columns by clicking in the column heading. The table columns are
| Chain:Num | Chain name and residue number | |
| Type | Residue type | |
| Residue Fit | Measure of the density fit for the entire residue | |
| Backbone Fit | Measure of the density fit for the backbone atoms | |
| Side Chain Fit | Measure of the density fit for the side-chain atoms | |
| Refine | Checkboxes to select side chains for refinement. You can use shift-click to select a contiguous set of rows. |
Update the density fit data in the table. Update updates the data for the selected residue, and Update All updates the data for all residues.
Exports the table contents to a formatted plain text file.
This button deletes the selected residue. It is mainly useful for deleting waters that are misplaced. If you delete a protein residue, you will have to build it back in again.
Color atoms by the value of the density fit. The colors range from dark green for the best fit through yellow to white for the worst fit. Residues colored white are therefore good candidates for further refinement. This color scheme is available as a regular Maestro color scheme, provided the density fit has already been calculated.
Refine the side chains that were selected in the Refine column of the table. Opens the Real-Space Refinement panel with Predict side chains chosen from the Method option menu, and the side chains selected in the Residues for side chain refinement section.
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