When opening a ccp4 map from EDS the map isn't well aligned onto the structure

[pschmidtke]

Hi,

when trying to visualize the structure 4o71 and others (3q0r etc) using an input pdb file and density (2Fo) from the pdbe we can observe that the map is not well centered on the structure itself. Also only a single cell is shown.

I noticed that the NGL code doesn't do symetry operations that can be specified in the ccp4 format, but this isn't the only issue here, as 3q0r also isn't displayed properly.

Any idea on what needs fixing here?

I investigated the symetry operations a bit and found source code in uglymol treating this, but didn't manage to make it work for now.

[fredludlow]

Hi @pschmidtke, it'd be nice to handle symmetry operations - I've never tried to implement this, but happy to look at some code and see if it's possible

[rowanwalker96]

Hi there @pschmidtke,

I had a similar issue and solved it first by converting the experimental data to MTZ file format:
https://www.rcsb.org/docs/general-help/x-ray-electron-density-maps#converting-experimental-data-to-mtz-file-format

Then I used the command phenix.mtz2map <mtz_file> <pdb_file> to generate the ccp4 map. Importantly, specifying the pdb file gives it something around which to draw the map!
https://phenix-online.org/documentation/reference/mtz2map.html

Would you be able to share your code to generate the above output? I usually work with nglview in a python notebook, but have been trying to convert a system like this into html so I can embed it (unfortunately nglview.write_html is unsuccessful in doing so).