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Protein Preparation Wizard Panel |
The purpose of this panel is to locate and fix structural defects in imported protein structures and prepare them for use by various Schrödinger products.
To open the Protein Preparation Wizard panel, you can:
Choose Applications → Protein Preparation Wizard in the main window.
Click the Prep Wiz button on the Project toolbar in the main window.
Choose Tasks → Protein Preparation in the main window.
You can also automatically open the Protein Preparation Wizard panel by setting the preference Open Protein Preparation Wizard after importing PDB file under Project – Importing structures in the Preferences panel.
The Protein Preparation Wizard allows you to take a protein from its raw state, (which may be missing hydrogen atoms and have incorrect bond order assignments, charge states, or orientations of various groups) to a state in which it is properly prepared for calculations using Schrödinger products such as Glide, Prime, QSite, Liaison, and MacroModel.
The intended workflow in this panel is from left to right: fixing structures first, then deleting unwanted chains and waters, then fixing or deleting het groups, and finally performing some optimization of the fixed structure.
Because automatic procedures cannot cover all possible cases, it is very important to check the correctness of the structure before using it for other applications. The Wizard helps you to do this by allowing you to step through various parts of the system and check their correctness.
Note: The Protein Preparation Wizard works on the structure that is displayed in the Workspace. You should ensure that this is the desired (and only) structure displayed.
There are several points in the workflow at which you can delete waters, based on various criteria, which are listed below:
Waters that are beyond a specified distance from het groups, in the Import and Process tab.
Waters that have nothing other than waters within a specified radius, in the Review and Modify tab.
Waters that have fewer than a specified number of hydrogen bonds to non-waters, in the Refine tab.
Manually selected waters, in the Review and Modify tab.
This panel has three tabs in which the main work is done. These tabs are described in other topics, which are linked below. The remaining features are described in this section.
In this text box you can specify the job prefix for the jobs run by the wizard, so that the files generated in the protein preparation process can be uniquely named.
Choose the host that you want to use to run preparation jobs, such as H-bond optimization and Impref minimization.
These options correspond to the options on the Display button menus on the Display atoms toolbar. If hydrogens are added later, they are displayed according to the options selected here. It is useful to display only the polar hydrogens when checking hydrogen bonds, for example.
Opens the Protein Preparation - Problems dialog box, which displays information on problems found with the protein that should be addressed.
Display a per-residue report on various properties of the protein, such as steric clashes, distance and angle deviations, G factors, B factors, planarity, stereochemistry. Opens the Protein Reports panel.
Display a Ramachandran plot of protein dihedrals. Opens the Ramachandran Plot panel.
Reset all settings to their default values, clear out all data, and return to the Import and Process tab.
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