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

[Tom Goddard]

I have fixed the mlp command so it can directly color volume surfaces -- will be in tonight's ChimeraX builds.

	Tom


> On Feb 13, 2021, at 1:06 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> You can color a cryoEM map surface #2 directly using
> 
> 	coulombic #1 surface #2
> 
> and also mlp should work
> 
> 	mlp #1 surface #2
> 
> but the mlp command has a bug that prevents that from working -- I will fix it next week.
> 
> 	Tom
> 
> 
>> On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337 at cam.ac.uk <mailto:ym337 at cam.ac.uk>> wrote:
>> 
>> 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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