Prime User Manual - ISP

Chapter 7: Prime–Refinement
If your structure does not meet one or more of the conditions outlined above, you must fix it
before you can successfully run a refinement. Some of the problems only become apparent
when you have run a refinement job, so it can be a useful diagnostic procedure to run a Prime
energy calculation first. This job is quick, and produces warnings in the log file, which you can
check in the Monitor panel.
Many of the preparation tasks are performed automatically or interactively with the Protein
Preparation Wizard. The Protein Preparation Wizard panel can be opened from the Workflows
menu on the main toolbar. When the preparation has finished, you should check that all
changes made are correct. You can fix any remaining errors with the procedures below. For
more information on the Protein Preparation Wizard, see the Protein Preparation Guide.
Procedures for fixing bond orders, formal charges, and atom names are given below. These
procedures use the Build toolbar and the Build panel, which you can display by clicking Show/
Hide the Build toolbar on the main toolbar or opening the panel from this button menu.
To assign bond orders:
1. Choose Assign Bond Orders from the Tools menu.
2. Inspect the residues in the structure for any remaining bond orders that are incorrect.
3. If there are still incorrect bond orders, click the Increment bond order or Decrement bond
order button on the Build toolbar.
4. Click the bonds in the Workspace structure that needs correction.
You can also right-click the bonds in the Workspace structure, and choose the correct
order from the Order submenu of the shortcut menu.
To view and change formal charges:
1. From the Label atoms button menu on the main toolbar, choose Formal Charge.
Charges are displayed for atoms that are charged.
2. Click the Increment formal charge or Decrement formal charge button on the Build toolbar.
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