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

[Y. Mutum]

Hi Tom

Thanks for this.

I've realised that the electrostatic calculation doesn't work, if there are posttranslationallymodified residues. In the case of pdb:6g2j for example, there's 2MR (dimethylated arginine). Could we please have a fix for this too?

Thanks
Yaikhomba

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________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Saturday, February 13, 2021 9:06:59 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

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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