[phenixbb] Help with using FFT map coefficients tool

Pavel Afonine pafonine at lbl.gov
Mon Jun 1 09:36:57 PDT 2015

Hi Emily,

ok, let's do it step-by-step:

1) Other tools -> Fetch PDB data, In Action choose "Download all data 
and convert CIF to MTZ".

This will give you model and reflection data.

2) Maps -> Calculate maps

Load model (PDB) and data (MTZ) files.

3) Maps -> FFT map coefficients, load *_map_coeffs.mtz file and run.

This will give *.ccp4 maps that you need.

I just did these steps and it worked for me fine.


On 6/1/15 8:49 AM, Emilia C. Arturo (Emily) wrote:
> Pavel,
> The command line steps you gave worked well (i.e. I got the map I 
> wanted) for the models in which I am interested.
> But the GUI is still giving the same error "This reflections file does 
> not appear to contain any suitable map coefficients", even for the PDB 
> id you gave as an example (1AKG). This is what I did to use the GUI: I 
> typed in the PDB id to the GUI 'Reflections tools' > 'Import CIF 
> structure factors' tool, and the tool fetched the model and .cif file 
> and output an mtz file. But when I loaded this mtz file into the GUI 
> 'Maps' > 'FFT map coefficients' tool, I got the error. Furthermore, 
> EVEN if I loaded the mtz file that I'd generated using the command 
> line phenix.maps 1akg.{pdb,mtz} into the GUI maps tool, I get the same 
> error.
> I am fine using the command line, but I suspect that there's an issue 
> with how the GUI is loading the mtz files for the Maps tool.
> Regards,
> 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
>     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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