[phenixbb] Converting .mtz to xplor or having phenix output to xplor file

Nathaniel Echols NEchols at lbl.gov
Wed Oct 28 11:08:34 PDT 2009

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
NEchols at lbl.gov

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