[phenixbb] how to generate sharpened map for input into Pymol

Daqi Tu dtu at red.dfci.harvard.edu
Sat Apr 24 11:23:38 PDT 2010

I found a convoluted way. Input Phenix map coefficients into CCP4 program 
CAD, apply negative B factor scaling. Then input resulting mtz file into 
CCP4 program FFT to generate CCP4 style map which Pymol can also read. I 
have not tried the new Phenix command line tool phenix.maps and do not know 
if it has B-factor sharpening option.  But would be nice to have it, like in 
CNS 1.2.


From: "Daqi Tu" <dtu at red.dfci.harvard.edu>
Sent: Saturday, April 24, 2010 10:16 AM
To: <phenixbb at phenix-online.org>
Cc: <dtu at red.dfci.harvard.edu>
Subject: how to generate sharpened map for input into Pymol

> Hi,
> I am generating a electron density map figure in pymol for my structure.
> Since the data is very anisotropic, map sharpening has proven to be quite
> useful. The structure was solved using Phenix. How do I generate an Xplor
> style map in Phenix that incorporates sharpening?
> Thanks.
> Daqi Tu
> Postdoc
> Eck lab
> Dana-Farber Cancer Institute

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