[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.
Pavel
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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