Protein Reports Panel

• Summary
• Opening the Protein Reports Panel
• Using the Protein Reports Panel
• Protein Reports Panel Features

Summary

This panel displays reports of various properties of the protein displayed in the Workspace, by residue.

Opening the Protein Reports Panel

To open the Protein Reports panel, you can:

• Choose Tools → Protein Reports in the main window.

• Choose Tasks → Protein Analysis → Protein Reports in the main window.

• Click Protein Reports in the Protein Preparation Wizard panel

Using the Protein Reports Panel

You can use this panel to identify residues that have certain characteristics. Selecting residues in the table marks them in the Workspace and zooms in on them.

Protein Reports Panel Features

• Display menu
• Export and Export All buttons
• Protein report table
• Structure average text box
• Update button

Display menu

This menu lists the various protein properties for which reports can be generated. When you choose an item, the table is updated with the relevant report. The items are described below.

Steric Clashes

Ratio of the interatomic distances to the sum of the atomic (van der Waals) radii from the force field. The threshold is 0.85.

Bond Length Deviations

Deviation from the ideal value derived from Engh and Huber. The RMSD is reported at the bottom.

Bond Angle Deviations

Deviation from the ideal value derived from Engh and Huber. The RMSD is reported at the bottom.

Backbone Dihedrals

G-factors for backbone dihedrals (see below for definition), along with dihedral angles. Less negative (closer to zero) means that the combination of angles is more probable.

Sidechain Dihedrals

G-factors for side-chain dihedrals (see below for definition), along with dihedral angles. Less negative (closer to zero) means that the combination of angles is more probable.

G-Factor Summary

G-factors for backbone dihedrals, side-chain dihedrals, and the sum of the two.

Average B-Factors

Average B-factors (temperature factors) for the backbone and the side chain for each residue, and their standard deviations.

Gamma-Atom B-Factor

B-factor for the gamma atom in each residue.

Peptide Planarity

RMSD of the atoms in the peptide linkage from the plane that minimizes the RMSD.

Sidechain Planarity

For side chains that have nominally planar groups, RMSD of the atoms in the planar groups from the plane that minimizes the RMSD.

Improper Torsions

For side chain atoms that are nominally planar, RMSD of the improper torsion for these atoms.

C-alpha Stereochemistry

Stereochemistry of the C-alpha atoms.

Missing Atoms

Residues for which atoms are missing from the structure.

G-factors are calculated by binning the dihedral angles from a collection of high-resolution structures into 10-degree ranges, and calculating the probability of a pair of angles lying in a given range. The G-factor is the logarithm of this probability. If there are no values in a given range, the G-factor is reported as "disallowed".

Export and Export All buttons

Export the report to a plain text file. Export exports the current report; Export All exports all reports. Opens a file chooser so that you can specify the file name for the report.

Protein report table

The table displays the residue label in the first column, and the report data in the remaining columns. Clicking a row marks the residue or the relevant part of the residue in the Workspace, and zooms in on the residue. Clicking a column heading sorts the table by the data in the column. Repeated clicking cycles through ascending order, descending order, and original order.

Structure average text box

Displays the average of the property for the entire protein structure, where applicable. Noneditable.

Update button

Analyze the structure in the Workspace and fill out the report tables. Useful if the structure in the Workspace has changed.