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Rotamers Dialog Box |
In this dialog box, you can select the desired rotamer for each residue that is selected in the Workspace. If you are using PrimeX, you can select the rotamer that fits the electron density best.
To open the Rotamers dialog box, you can:
Choose Edit → Adjust → Rotamers in the main window.
Choose Rotamers from the Adjust button menu on the Edit toolbar.
Before you open the Rotamers dialog box, you must select one or more residues in the Workspace for adjustment. To do this, you can choose Residue from the Select button menu on the Edit toolbar, and select the residues.
You can also select the residues in the sequence viewer.
When you have a residue selection, open the Rotamers dialog box as described above. You can then choose a residue from the residues table. The Workspace view zooms to the chosen residue, and the rotamers are listed in the rotamers table. Clicking on a rotamer displays the rotamer in the Workspace. To return to the original conformation of the selected residue, click Restore to Input Conformation. Once you are satisfied that you have the desired rotamer, you can choose another residue for rotamer adjustment. When you have finished adjusting rotamers, click OK to accept the structural changes and exit, or click Cancel to return to the original structure.
If you want to change the rotamers that are displayed, you can do so by
copying the file rotamer.res from
$SCHRODINGER/mmshare-vversion/data to your
Maestro preferences directory, $HOME/.schrodinger/maestro##,
where ## is the two-digit Maestro version, and then editing the copied
file. A description of the syntax is given at the top of the file.
Lists the residues for which atoms are selected in the Workspace. The chain name, residue name, and residue number are given. You can select a single residue in the table. When you select a residue, the rotamer table is filled out with the rotamers for that residue. You can change the selection in the Residues table by clicking the row or the Next and Previous buttons. You can also use Alt+N (⌥N) and Alt+P (⌥P) instead of the buttons.
Select this option to perform a fit to Workspace for the selected residue. The option is stored as a preference, so the selection persists between Maestro sessions.
Lists the rotamers for the residue selected in the residues table. The table columns display the dihedral angles for each rotamer, as well as an index number and a percentage that represents a standard population for the rotamer. The initial value of the dihedrals is shown in the first row, and labeled original. If you have a density map from PrimeX and click Choose Best Fit, a measure of the density fit is displayed in the Fit column. Smaller numbers represent a better fit. The Clash column indicates with a + sign whether there are bad contacts between the rotamer and atoms in adjacent parts of the structure.
Selecting a row in the table displays the rotamer in the Workspace. When you click OK, this rotamer (and any other rotamers you selected) replaces the original. You can change the selection by clicking the row or the Next and Previous buttons below the table; you can also use Alt+E (⌥E) and Alt+R (⌥R) instead of the buttons.
The rotamers are ordered by the population by default. You can sort the rows by the value in any column by clicking on the column heading. Clicking repeatedly in the column heading cycles through ascending order, descending order, and original order. The table cells are noneditable.
Restore the conformation of the current residue to the input conformation.
If you select this option, the rotamers are displayed as the density fit calculation is done when you click Choose Best Fit.
If you are running PrimeX and have a 2Fo-Fc or 3Fo-2Fc density map, you can click this button to choose the rotamer that best fits the electron density. (Other map types may give erroneous results.) Rotamers that have bad or ugly contacts with the rest of the structure are not considered for the best fit.
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