[phenixbb] Converting .mtz to xplor or having phenix output to xplor file

Nathaniel Echols NEchols at lbl.gov
Tue Oct 27 14:54:29 PDT 2009

On Oct 27, 2009, at 2:28 PM, Sam Stampfer wrote:
> This isn't exactly phenix-related but someone might know an easy  
> solution.  I'm trying to open an electron density map in pymol.  It  
> won't open .mtz files and the .xplor files I generated from ccp4i  
> don't seem to work either.  I need to have my density as a .xplor  
> file in order for pymol to open it (I think).  How would I generate  
> a .xplor file from .mtz?  Or, alternately, how can I set phenix to  
> output a .xplor file?  I've had it output to a cns file instead  
> of .mtz but that didn't help me get it in .xplor format.

Several solutions:

1) phenix.create_maps

2) output.write_maps=True in phenix.refine will generate XPLOR maps.

3) In the GUI, it should create the XPLOR maps on the fly if you click  
one of the "Open in PyMOL" buttons.

Since most of the necessary code is already floating around, I don't  
mind creating a utility for simply converting map coefficients, if  
people would find this useful, but unfortunately we don't have the  
ability to write CCP4-format maps yet.

One thing to make sure of is that PyMOL is recognizing the input  
format correctly - sometimes you need to explicitly state this:

PyMOL> load 2fofc.xplor, format=xplor

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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