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Protein Preparation Wizard — Import and Process Tab |
In this tab you can import a structure if there is not already a structure in the Workspace, select options to amend the structure, and perform the basic preparation tasks.
Note: You should always check that the structure is correct after any automatic procedure is run.
The Protein Preparation Wizard uses the structure in the Workspace as its input. The import controls are provided so you can conveniently load a structure from an external source. These allow you to obtain a protein structure from a file or from the PDB. The structure is imported into the project as a project entry, and replaces the Workspace.
Enter the PDB ID of the protein you want to retrieve in this text box.
These options allow you to choose extra data from the PDB to download along with the structure:
Diffraction data option— Select this option to download the X-ray diffraction data as well as the structure. This is particularly useful for PrimeX.
Biological unit option— Select this option to download the biological unit from the PDB rather than the regular PDB file. All structures in the biological unit are merged into a singe project entry on import. This option requires an internet connection.
Alternate positions—Select this option to include alternate positions of the atoms in the structure. By default only the highest occupancy position is downloaded.
Click this button to import the specified protein from your local copy of the PDB, with a fallback to downloading from the PDB web site. If you want to download the protein from the PDB web site, you can use the Get PDB File dialog box to download the file, then import it by clicking Browse in the Protein Preparation Wizard panel.
Clicking this button opens the Import panel, in which you can navigate to the desired file and import it.
In this section you select options to amend the structure and perform the basic preparation tasks. A new entry is created for the preprocessed structure, which is colored by element.
Align the protein structure to a reference structure using the
structalign program, with the default settings. This option has two
associated options for selection of the reference structure:
See the Protein Structure Alignment Panel topic for more information.
Assign bond orders to all bonds in the structure, including het groups. This option performs the same task as Assign Bond Orders on the Tools menu.
Add hydrogens to all atoms in the structure that lack them. The hydrogens
are added by the utility applyhtreat.
Remove the original hydrogens before adding hydrogens to the structure. This option allows any problems with hydrogen atoms in the original structure to be fixed, including nonstandard names, which prevent proper H-bond assignment.
Break bonds to metals and corrects the formal charge on the metal and the neighboring atoms, then add zero-order bonds between the metal and its ligands, so that it is still considered part of the same molecule.
Find sulfur atoms that are within 3.2 Å of each other, and add bonds between them. CYS residues are renamed to CYX when the bond is added. This option is selected by default.
This option converts selenomethionines (MSE) to methionines (MET), and is not selected by default. A dialog box opens to inform you if any conversions are done.
Run a Prime refinement job (refinestruct) to place and
optimize the missing side chains.
See the Predict Side Chains Panel
topic for more information.
Fill in missing loops from the SEQRES records in the PDB file. Requires Prime. The resulting loop may not be of high quality, and a Prime loop refinement should be performed to obtain higher quality. See the Refine Loops Panel topic for details.
Add ACE (N-acetyl) and NMA (N-methyl amide) groups to uncapped N and C termini. These termini include any chain breaks.
Delete waters that are more than the specified distance (in angstroms) from any het group.
You can also delete waters individually in the Review and Modify tab, and you can delete waters that do not form H-bonds with non-waters in the Refine tab.
Prepare the structures using the options selected in this section. The progress of the structure correction is displayed at the foot of the panel. When all operations are finished, a new entry is created and a color scheme is applied to the structure. The tables in the Review Structure tab are filled in, and if any problems are found with the structure, the Protein Preparation - Problems dialog box is displayed, listing the problematic atoms or residues.
Open the Protein Preparation - Problems dialog box, which contains tables of residues that have missing atoms, overlapping atoms, and atoms that are incorrectly typed. The Workspace structure is analyzed to detect these problems before opening the dialog box. You can click on a row in any of the tables in the dialog box to zoom in on the atoms or residues listed in that row. To fix a problem, you can use any of the Maestro capabilities.
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