[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
510-486-5136
NEchols at lbl.gov
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