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 necessary.
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.

Pavel

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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