PrimeX Basics: Modifying Structures

When you modify a structure in the Workspace, the changes are also made in the project entry to which the structure belongs. This is the default behavior. You can change this behavior in the Project tab of the Preferences panel, under Synchronize Workspace changes, so that changes in the Workspace are only propagated to (“synchronized with”) the entries when you request it. This is convenient when you want to experiment with a structure, for example. However, you should be careful to reset the preference when you want changes to be saved automatically again. When there are unsaved changes in the Workspace, a button for saving changes is displayed in the status bar.

An alternative to changing the preference is to create a new entry with the Workspace contents when you want to experiment with a structure. You can do this with the Checkpoint button in the PrimeX panel. To do so you must have a reflection file as well as a structure, since checkpointing associates the structure with the reflections as well as creating a new entry. Any changes already made to the structure are associated with the new entry if the Workspace contents have not been synchronized. The checkpoint function can thus act as a multi-step undo function, by deleting entries from the latest one saved.

Maestro provides a number of other tools for modifying structures, many of which are available from the 3D Builder panel, which you open from the toolbar or the Edit menu.

One of the useful features available from the 3D Builder panel and the selection shortcut menu is the ability to mutate the standard residues, which you might want to do on an individual basis rather than use the Mutate Model to Sequence Dialog Box.

To mutate a residue:

  1. Right-click on the residue you want to mutate.

    You can click on the residue in the sequence viewer so that it is selected in the Workspace, or use the feedback in the status bar to identify the residue.

  2. Choose Mutate from the shortcut menu, then click on the name of the residue you want to mutate to in the box that is displayed.

To place a solvent molecule or ion:

  1. In the 3D Builder panel, click Add Fragments, then click the ... button to open the Fragments panel.

  2. Choose Protein Ions & Solvents from the Fragments option menu.

  3. Click on the button for the molecule or ion you want to place.

  4. Click in the Workspace at the location you want to place the molecule or ion.

Make sure you don’t click on an atom. If you have a map displayed you can click on the corresponding density peak. The centroid of the ion is placed at the pointer position, with a z coordinate of zero (the z axis is perpendicular to the screen). You will probably need to adjust the positioning of the fragment that you placed and optimize its location. For automatic placement in a density peak, use the Ligand/Solvent Placement Panel.