Advanced Ion Placement Dialog Box
In this dialog box you define regions to be excluded from ion placement and candidate regions for ion placement.
To open this dialog box, click Advanced ion placement in the Ions tab of the System Builder panel.
- Features
- Additional Resources
Advanced Ion Placement Dialog Box Features
- Candidates list
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Lists the candidate residues for placement of ions. Control-click rows in the table to select the residues for which you want ions to be placed. The charged atom on the selected residue is displayed in CPK and colored red in the Workspace. The number of ions placed (initially 0), the number of ions remaining to be placed to fill the number specified in the Ions tab (e.g. to neutralize the system), and the total number of candidate residues, are displayed above the list.
The residues that are selected when you click OK are the ones for which ions will be placed when the model system is built. The ions are placed near these residues, replacing a solvent (water) molecule.
- Candidates button
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Automatically find candidate regions to place the ions and fill the table with these candidate regions. When positive [negative] ions are selected, negatively [positively] charged protein residues are shown in the tables. These candidate regions do not include the excluded region defined in the Excluded region section of the Ions tab.
- Select button
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Open the Atom Selection Dialog Box to define other candidate regions (residues) to locate ions. The new regions are added to the table.
- Reset button
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Remove all rows from the table.