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

[Y. Mutum]

Hi Elaine

Thanks - both your suggestions on deleting surfaces to regain the speed, and this point about coloring the cryo-EM map works.

Yaikhomba
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 13 February 2021 17:10
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential

The "coulombic" command to calculate ESP does not yet have an option to create a map model, sorry.

Elaine

> On Feb 13, 2021, at 9:09 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Yaikhomba,
> It doesn't make any sense to color the atoms by MLP... the point of the MLP calculation is to combine all the atomic contributions into a potential that other molecules would "see" at the surface of the protein.  I could say exactly the same thing about ESP (electrostatic potential).  The values of ESP at the centers of same atoms used to compute the ESP are singularities (i.e. infinity if you ignored the effects of discretizing the calculation on a grid).  In other words, the location is important and you definitely don't want the values from the atomic centers.
>
> However, it sounds like your ultimate goal is to apply the coloring to the isosurface of a cryoEM map instead of the atomic structure's molecular surface.
>
> To do that you first create a map file of the MLP (mlp command with map true), and then use that map to color the isosurface of the cryoEM map with the "color sample" command.  In that command, surf-spec is the cryoEM map model, and then map map-model gives the MLP map.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Feb 13, 2021, at 6:07 AM, Y. Mutum <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.
>>
>> Any workaround suggestions would be helpful for electrostatic too.
>>
>> Thanks
>> Yaikhomba
>

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