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Protein Preparation Wizard — Review and Modify Tab |
In this tab you can inspect parts of the structure in the Workspace by selecting them in tables, deleted unwanted parts, and generate ionization, tautomeric, and metal-binding states for het groups.
When you select a chain, water, or het group, the color scheme with green carbons is used for the selected atoms, and the color scheme of the unselected atoms is changed to darker colors so that the selected atoms stand out. The selection also computes and displays hydrogen bonds between the selected and the unselected atoms.
Analyze the Workspace structure to identify chains, waters, and het groups, and fill the tables with the results. If you clicked Preprocess in the Import and Process tab, the analysis is done automatically. This button is intended for working with structures that have already been preprocessed to fix any issues with the structure.
Fit the selection to the size of the Workspace when you select chains, waters, or hets.
Display only the selected chains, waters, and hets.
Select this option to pick chains, waters, or hets in the Workspace. The picked objects are selected in the tables. You can use shift-click to add to the selection and control-click to change the selection of an object without affecting the selection of other objects.
Delete the selected chains, waters, and hets.
Select het groups and waters within the specified distance of the chains that are selected. This feature is useful for reducing a multimer to a monomer: select the chain, select the het groups/waters, invert the selection and then delete.
Select waters that have nothing other than waters within 5 Å.
Invert the selection of chains, waters, and hets. This is useful for selecting the parts that you want, then deleting the rest (by inverting the selection, then clicking Delete).
This table lists the chains in the Workspace. The chains are listed by the chain letter, with a blank name shown in quotes. You can select multiple chains in the table for application of an action.
This table lists the waters in the Workspace. A serial number and the residue number are given in the table. You can select multiple waters in the table for application of an action.
This table lists the het groups in the Workspace. A serial number and the het name are given in the table by default. The het name consists of the chain name, residue name, and residue number for each residue in the het group. You can select multiple hets in the table for application of an action.
When ionization and tautomeric states have been generated, Sn (state) columns are added to the het groups table and are populated with check boxes for the selection of the state. The column for the original state is marked Orig. The selected state is displayed in the Workspace, with markers to indicate the atoms that differ between states. When you select a state, the status area at the foot of the panel displays the state penalty, the tautomer probability, the charge, and the number of hydrogen bonds made to the het group. The state that is selected by default is the state with the lowest penalty (and if there is more than one such state, it is the state with the most H-bonds).
Run Epik to generate probable ionization and tautomeric states in the pH range specified for all het groups. The calculation may take a few minutes. When it finishes, the table rows for the het groups are populated with check boxes, which you can use to select the desired state. The het states are labeled with formal charges on charged atoms.
When Epik is run, include generation of states for binding to metals in metalloproteins.
Enter the target pH and pH range for the generation of probable ionization and tautomeric states in these text boxes.
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