[phenixbb] autosol output to electron density figure in pymol

Pavel Afonine pafonine at lbl.gov
Wed Mar 5 08:15:18 PST 2008

Hi Shivesh,

this is what I usually do: manipulate the structure in Coot and make 
publishable pictures in Pymol. To do this, just take the output from 
Autosol and run phenix.refine - it will produce the Xplor formatted maps 
that you can use in Pymol:

% phenix.refine overall_best.pdb data.mtz

where data.mtz is you data file containing Fobs, freeR flags (please do 
not confuse it with map coefficients file 
overall_best_refine_map_coeffs.mtz). By default it will produce two 
files (with .map extensions) one containing 2mFo-DFc and another mFo-DFc.

You can also ask phenix.refine to produce any number of maps with other 
coefficients, for example 3Fo-2Fc, 3.3Fo-2.2Fc, etc. (for this you will 
need the latest version of phenix.refine currently available from CCI Apps).


shivesh kumar wrote:
> Dear all,
> I have an overall_best.pdb and  overall_best_refine_map_coeffs.mtz 
> file as an output file from Autosol.When I open this in coot I see the 
> nice density.How can make a figure with density using pymol.Thanx in 
> advance for the suggestions.
> Shivesh
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