[phenixbb] offtopic: Problem with Pymol showing maps

Pavel Afonine PAfonine at lbl.gov
Fri May 28 20:58:01 PDT 2010

Hi Tanya,

> I have several maps from Phenix and want to draw some pictures in 
> Pymol. I am opening the files, renamed to ccp4 or map, or not, 

I'm slightly puzzled about this... Are you trying to open X-plor 
formatted maps? By default phenix.refine writes out only MTZ with map 
coefficients. Basically, my question is: how you obtained the maps that 
you are trying to see in PyMol?

> If you know some nice simple program to do nice pictures of the 
> electron densities- share your knowledge please!

I always use PyMol for this - it is simple, and you can find all basic 
commands and temples on the web.


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