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Interactive H-Bond Optimizer Panel |
This panel is used to interactively assign orientations of hydrogen-bonded groups in proteins (including waters) and of the imidazole ring in His and the terminal amides in Asn and Gln.
To open the Interactive H-Bond Optimizer panel, you can:
Click Interactive Optimizer in the Refine tab of the Protein Preparation Wizard panel.
Click Optimize H-Bond Networks in the PrimeX panel.
This panel can be used from the Protein Preparation Wizard panel to check on the assigmnents of hydrogen orientations in the hydrogen-bonding network and the His, Asn, and Gln orientations. Each hydrogen bond donor, His ring, and Asn and Gln terminal amide is considered a separate orientable species.
In this section you perform the analysis of the system into hydrogen-bonded clusters.
Set the pH value for determining the protonation state of protein residues.
Use PROPKA to predict the pKa values of the protein and determine the protonation state at the specified pH. If you deselect this option, a set of simple rules is used to determine the protonation states according to the pH range:
Label protein atoms with their predicted pKa values.
Analyze the hydrogen bonds in the structure, subject to the options that are selected in this section, to generate the species and clusters and their states, which are then listed in the table. You must click this button when you first open the panel, or if you add or delete bonds or atoms in the Workspace or include a new structure in the Workspace. The analysis can take a minute or so, depending on the size of the system.
Include the current orientations of the hydrogen-bonded species among the orientations to be sampled.
Restrict the scope of the analysis to the atoms that are selected in the Workspace.
When analyzing the Workspace structure, use crystal symmetry to include in the analysis any H-bonds to atoms in neighboring cells. This can be important if only part of the biologically-relevant structure is present in the asymmetric unit. Using this option can significantly increase the time taken in the optimization.
There are two options for display of species in the species table, with relevant controls. The content of the species table depends on the option that is selected.
View all species—list all species in the table. The number of species is given to the right of this option.
View cluster—list the species for the specified cluster in the table. You can enter the desired cluster number in the text box, use the arrow buttons to step through clusters one at a time, or use the double-arrow buttons to go to the beginning or end of the cluster list. The number of clusters is given to the right of this option. When you select a cluster, the Workspace view zooms in to the cluster, its carbon atoms are colored green, and any alterations to the state are labeled. The H-bonds in and to the cluster are also shown in the Workspace.
This button zooms in on the cluster so that the cluster fills the Workspace.
Optimize the orientations of the species listed in the table. When the optimization has finished, the Display result controls become available, and the best-scoring result is displayed.
The text box shows the index of the result that is displayed in the Workspace. The index starts from 0, for the lowest (best) score, and the results are ordered by score. To change the display, you can enter an index in the text box, or use the arrow buttons to step through the results. When you change the result that is displayed, the orientation of the species in the Workspace is changed, and the State column of the species table is updated to indicate which state of each species is represented in the chosen result. The score for the result is displayed to the right of the text box, and is updated as you step through results for the cluster or manually change the state via the species table.
This table lists the orientable species for the choice of view made at the top of the panel. The table is noneditable, but can be used to select a species to change its orientation. You can select a single row of the table to adjust the orientation of the species. When you select a row, the species is centered in the Workspace and the view zooms in to that species, whose carbon atoms are colored green, and a label is added if its orientation has changed. The UP ARROW and DOWN ARROW keys can be used move the selection up and down the table.
The table is deactivated if you delete or add atoms or bonds in the Workspace. The species and their states can be recalculated by using the Analyze Network button.
The table columns are as follows:
| # | Index of species, relative to the full list or the cluster, depending on the choice of view option. | |
| Lock | Option to lock the orientation of the species at the current state. The space bar can be used to lock or unlock the orientation. When you lock the orientation, it is not changed when you click Optimize. If you manually change the state, the lock does not lock the manually-adjusted state but the original state. You can add a manually-adjusted state to the set of states for the species with the Add Orientation button. | |
| Species | Identity of species, given as the chain name followed by a colon, the residue name and number, and another colon and the atom name if a rotatable hydrogen is involved. | |
| State | This column indicates the state of the species:
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| Arrow buttons | These buttons allow you to cycle through the states for the selected species. |
Adds the current orientation of the species to the list of states. The states added using this button are labeled User n, where n is an index that starts from 1. This button allows you to perform manual adjustments, and have those adjustments included for sampling and locking. The button is only available for rotatable hydrogens and waters.
Sort the table by the values in the State column. The sorting is temporary: if you switch to display a different cluster or to display all species, then the sort must be re-applied.
Select this option to pick an atom in the Workspace that belongs to a species of interest. The cluster that the species belongs to is loaded into the species table. The species is selected and centered in the Workspace, its carbons colored green, and labeled if its orientation has changed.
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