In our project we are exploring multiple ligands docking to protein. Is it possible to color protein or its solvent accessible surface area according to distances to docked ligands.
I found Gromacs mdmat for distance maps, but converting multiple ligand topologies and then using xpm-file information for SASA coloring is a bit time-consuming. Ideas, please?
Python & PyMOL:
1. Measure interatomic distances between ligand and protein.
2. Normalize the distances (0 to 100 scale).
3. Put the normalized distances into the B-factor column of the PDB file.
4. Load the PDB file with the normalized distances into PyMOL, show the protein in surface representation and color the protein by B-factors.
https://pymolwiki.org/index.php/Spectrum
This may be useful of what you need https://freesasa.github.io/python/
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