On Oct 28, 2009, at 10:58 AM, Young-Jin Cho wrote:
When I did phenix run, it made .map files that were not readable in my Pymol. I don't know this is the case for everybody. However, once I changed .map to .xplor, there was no problem.
This is why you need to do this: PyMOL> load something.map, format=xplor Otherwise, it assumes that the extension .map is a different format (not sure which one, but definitely not XPLOR).
Another follow up questions is how you can make difference map with positive and negative density maps showed up separately or together in Pymol as we see on the coot.
isomesh neg_diff, map_name, -3.0 isomesh pos_diff, map_name, 3.0 Although you're probably going to want to add another parameter for the selection to draw around, otherwise I think it tries to draw the entire map, which is often too much for the graphics card to handle. Unfortunately, the way it deals with re-centering and maps isn't very robust compared to Coot. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]