Creation of maps with structure properties - Electrostatic potential, charge, hydrophobicity/polarity, ...

[crisfbazz]

Hello! Thanks for this great library that eases manipulating X-ray crystallographic data! It made a difference in my work!

I would like to know if there is an ease way to create maps with some structure properties such as the electrostatic potential, charge, polarity and hydrophobicity of the molecules. The idea here is to use the protein structure (.cif/.pdb files) to retrieve their atoms or residues, compute the desired propertie, and with it generate a map, in ccp4 format, similar to the electron density map, but with values equal to the properties values for the respective structure. This way, in each position of my crystal I would be able to retrieve not only its density value, but also the calculated properties (charge, polarity, hydrophobicity, etc) from the maps populated with that information. This would allow to visualize these crystal properties together with the density values and help in some analysis (for ligand interpretation, analyzing binding sites, others).

These properties can be visualized with pymol and are described here: https://research.uni-leipzig.de/straeter/pymol/pymol_map_properties.html

But I could not find a program that allows retrieving these data in a 3D grid similar to the electron density ccp4 map and in an automated way. This could add more information to the crystal data and ease reusing it to other purposes.

Could you help me figuring out how the best way to use Gemmi to create these maps with other properties of the structure, possible using algorithms similar to the ones used by pymol? This solution could be wrapped to new map functions of Gemmi, to manipulate and extract information from crystallographic data.

Hope we can move forward with this discussion! Thanks

[wojdyr]

From what I understand, the page you linked to shows how PyMOL can visualize properties of atoms, there are no ccp4 maps there. So you don't need to generate map files, all that PyMOL needs is a coordinate file.
Gemmi can generate maps of electron density (gemmi sfcalc --for=xray) and maps of electrostatic potential (gemmi sfcalc --for=electron). But I don't think anyone uses or generates maps of hydrophobicity or polarity.

[crisfbazz]

The ideia was to generate these ccp4 maps with the properties of atoms, which PyMOL only creates for visualization.
Thanks to point out how to create the electrostatic potential map, that will be useful.

These maps could be used most for visualization with other tools, and in my specific usage I would also try to use them as extra features of the crystal, but that is a specific usage indeed.

[wojdyr]

In general, it could be implemented, for example, using NeighborSearch, but it'd require some arbitrary assumptions of how the properties, such as charge or hydrophobicity change with the distance from an atom.

[crisfbazz]

That's what I imagined, it would require some function to apply the properties based on the atoms position and distance. I'll share it here if I manage to work on this. Thanks.