[phenixbb] Help with using FFT map coefficients tool

[Emilia C. Arturo (Emily)]

Paul and Pavel,

Thank you for bearing with me - I am still so new at this. I did some
side-by-side 'experiments' with the GUI and at the command line (now I know
about the reflection file editor tool, too) and now I understand what I'd
done wrong, and where I misunderstood things: I see now that the 'Import
CIF structure factors' tool converts the PDB data to "MTZ format", but even
though I'd supplied both the structure factors and the model (because there
are fields available in the GUI for both), this tool does not generate map
coefficients; I could have guessed as much from the name of the tool ;-).
Basically, I just needed to use 'Calculate map' after using the 'Import CIF
structure factors' tool.

Pavel, by the way: the command line 'phenix.maps 1akg.{pdb,mtz}' does also
generate a CCP4 format map, without explicitly requesting one.

I learned a lot in going through the exercise. Thank you :-)

Emily.

On Mon, Jun 1, 2015 at 12:36 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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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>>
>>
>>
>
>
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