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

[Y. Mutum]

Thank you Elaine, Tom and Eric.
Very helpful indeed!!
Yaikhomba

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________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, February 16, 2021 10:04:14 PM
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential

Hi Yaikhomba et al.

A brief cautionary note that when using the "surfaces" option, you may need to be more specific about which atoms to use in the calculation.  The "mlp" command automatically ignores non-protein atoms, so it's less likely to cause a problem, but "coulombic" does not, so bear in mind that if you give #1 it will try to include the charges of all atoms in #1, including solvent, ligands, etc.  It may needlessly try to calculate charges for nonstandard ligands (and sometimes fail) when you really meant only to consider the protein atoms.

So if #1 includes nonprotein atoms, instead of

coulombic #1 surface #2

it would be safer to give

coulombic protein surface #2

...to use all protein atoms, or you could also be more specific about the model and/or chain ID:

coulombic #1 & protein surface #2

coulombic #1/A & protein surface #2

I tend to forget this but then run into it when I'm actually trying to use the command, or put it in a tutorial!
Best,
 Elaine

> On Feb 16, 2021, at 12:00 PM, Tom Goddard <goddard at sonic.net> wrote:
>
> 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> 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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