[phenixbb] Help with using FFT map coefficients tool

Pavel Afonine pafonine at lbl.gov
Sun May 31 23:08:05 PDT 2015

Hi Emily,

step 1 - get files from PDB:

phenix.fetch_pdb 1akg --mtz

step 2 - compute maps:

phenix.maps 1akg.{pdb,mtz}

step 3 - convert map coefficients into map:

phenix.mtz2map 1akg_map_coeffs.mtz

Note 1: you can request to output actual maps at step 2, so step 3 isn't 
Note 2: all the above you can do in Phenix GUI.

Let me know if you still having problems with this and I will send 
step-by-step instructions how to do this using the GUI.


On 5/30/15 3:05 PM, Emilia C. Arturo (Emily) wrote:
> Hello.
> I'd like to generate a map appropriate for viewing in PyMOL, using a 
> model and structure factors downloaded from the PDB. But I'm unable to 
> do so, and perhaps you can help me figure out what I might be doing 
> wrong:
> To generate the map, I did the following using the phenix GUI (version 
> 1.9-1692):
> 1. I used Reflection tools > Import CIF structure factors to convert 
> the .cif format structure factors for PDB id 1J8U to an mtz file.
> 2. Then, to configure the job to generate the CCP4 map, I loaded this 
> mtz file, but when I did that I got the following error:
> "This reflections file does not appear to contain any suitable map 
> coefficients"
> I went through the same steps again for two other PDB ids, this time 
> generating the mtz file by either letting phenix do it from a PDB id, 
> or by supplying the tool with both a .cif file with structure factors 
> and a pdb model file. I get the same error.
> Has anyone any advice?
> Regards,
> Emily.
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