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Protein Preparation - Problems Dialog Box |
This dialog box contains tables that list problems found with the structure after preprocessing in the Protein Preparation Wizard panel.
To open the Protein Preparation - Problems dialog box, you can:
Click View Problems in the Protein Preparation Wizard panel.
The purpose of this panel is to list the problems found during processing of a protein structure, so that you can fix them before using the protein structure for other applications. You can make full use of other Maestro features while this panel is open: it only prevents interaction with the Protein Preparation Wizard panel.
When you have corrected any of the problems, you can click Update to redo the analysis of the problems and remove them from the tables. If all the problems are fixed, an alert box is displayed to notify you of this fact, and the Problems dialog box closes.
Information for each type of problem is presented in a separate tab. If there are no problems of a particular type, the tab is unavailable.
This tab lists atoms that have incorrect atom types. Click on a table row to select and zoom in on the problem atom. You can fix the atom type by using the Atom Properties tab of the Build panel. Choose Atom Type (MacroModel) from the Property menu, then select Set atom type (MacroModel). Choose the correct atom type from the list, then click on the atom that needs to be changed.
This tab lists residues for which atoms are missing. Click on a table row to select and zoom in on the residue that has missing atoms. If you want to add the missing side chains by running a Prime side-chain prediction job, click Add Missing Side Chains.
Another way of adding the missing atoms is to mutate the residue to itself. To do this, right-click on one of the residue atoms in the Workspace, and choose Mutate → residue from the shortcut menu. If you do this, the side chains might not be optimally placed. You can fix them with a Prime side-chain prediction. Another alternative is to choose a rotamer in the Rotamers dialog box (Edit → Adjust → Rotamers), and then do a minimization by selecting the residue in the Workspace and pressing Ctrl+M (⌘M).
This tab lists pairs of atoms that are too close (bad contacts). One way to fix these problems is to select the residue that contains the atoms (use the Select button on the Edit toolbar), or simply select the table row to select just the overlapping atoms, and press Ctrl+M (⌘M) to do a quick minimization.
If the atoms are superimposed, however (zero distance), this can indicate a duplicate het group, which you can delete in the Review and Modify tab of the Protein Preparation Wizard panel. Otherwise, you can use the Atom Selection dialog box to select one of the duplicates for deletion (Edit → Delete → Select).
When examining overlapping atoms, it is a good idea to ensure that all atoms are displayed. By default, only polar hydrogens are displayed, so you should select All hydrogens in the Protein Preparation Wizard panel, then open this dialog box.
This tab lists residues that have alternate positions in the input structure. Although these positions are legitimate, the protein preparation can only be done on a structure with a single set of coordinates, so you must choose one of the alternate positions for each residue.
To choose a position for a residue, first select the residue in the table. The view zooms in to the residue, and the default position is marked. Click Next Position to switch between positions. When the position that you want to keep is displayed, click Commit. The atoms in this position are kept, and the alternates are deleted.
Update the tables in the panel by rerunning the analysis of the problems. Problems that have been fixed since the last analysis should no longer appear in the tables. If there are no remaining problems, an alert box is displayed, and the Problems dialog box closes when you click OK.
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