On Mon, Jul 8, 2013 at 3:49 PM, Yarrow Madrona wrote:

1. We recently moved all of our data from one hard drive to another. However, we do not know how to change the directory for all of our projects. The directory is similar but the hard drive is now called tp3home instead of tp2home.

We found a .phenix directory that has a file with a list of projects and directories. We updated the directories but this did not make a difference in the GUI.

Yes, it is non-trivial at the moment. The most appropriate mechanism: - move ~/.phenix somewhere else (don't delete, just to be safe, but get it out of the way so a fresh database can be created) - open the GUI, set up a tutorial or temporary project just to get to the main GUI - under "Projects" menu, pick "Import project...", and pick the directory you want to import This should rewrite *most* of the paths, at least in configuration files.

2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually?

Not within the phenix.refine GUI, but I was intending to add this feature. Stay tuned. -Nat

On Mon, Jul 8, 2013 at 3:49 PM, Yarrow Madrona wrote:

2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually?

Okay, the next build (1426 or newer, as always depending on whether anything breaks tonight) will have an "Omit map" button in the Output tab, which lets you specify atoms which will have occupancies set to zero before refinement. On the command-line the equivalent parameter is omit_selection. The bulk solvent mask will not be extended to compensate. For composite omit maps, or iterative-build omit maps, you should still use AutoBuild (i.e. the separate omit map GUI). -Nat