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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