[chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential

[Y. Mutum]

Hi

I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant.

I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'.

First, I tried to generate a 'mlp' using the command:
>>> mlp #1 map true color true

Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it.

Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>.

Any workaround suggestions would be helpful for electrostatic too.

Thanks
Yaikhomba
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