[phenixbb] Simulated annealing composite omit map conversion

Nathaniel Echols nechols at lbl.gov
Sat Oct 8 19:11:10 PDT 2011

On Sat, Oct 8, 2011 at 6:23 PM, Yuri <yuri.pompeu at ufl.edu> wrote:
> I am calculating an SA. composite omit map to show active site density.
> It looks like the output format is mtz coefficients. How can I get it to
> ccp4 or .xplor format for PyMol?

If you're in the GUI, this happens automatically when you click one an
"Open in PyMOL" button.  If you're using the command line, use this
command to get the CCP4 map:

phenix.mtz2map map_coeffs.mtz model.pdb

The model file is optional, but providing it will result in a map that
covers your molecule instead of just the unit cell.  (This is also in
the GUI as "FFT map coefficients".)  Output is one .ccp4 file for each
set of map coefficients it finds - in most cases the file names will
reflect the MTZ column labels.  (Depending on which version you're
using and which columns AutoBuild outputs, the map coefficients will
be in either FWT,PHWT or FP PHI* FOM*.)


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