Hi Emilia, the process you described will give you an MTZ with the observed amplitudes (deposited in the PDB). You will need to generate phases from the model to make a map. Normally I would suggest using “Fetch PDB data” under “Other tools” and select the “Download all data and create maps” option. Alternatively you can use “Calculate Maps” in the Maps section to make a map using the model and data. I’m not sure why you can’t use "FFT map coefficients” on the 1akg_map_coeffs.mtz file (that should work). Maybe you can let us know what the array names and types are in that file. Cheers, Paul

On Jun 1, 2015, at 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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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 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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