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

[Y. Mutum]

Hi Tom

I forgot to add, in addition to the non-standard protein residues, there are also a couple of errors, attributed to terminal OH group not added. The ChimeraX version here is: 1.2.dev202102050202 (2021-02-05).

The commands I used were:
>>> open 5gup; open 9539 from emdb
>>> coulombic #1 surface #2

After this, I get this error (the residue list below is not complete, but I have left a few to help gauge the error):

The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics:
/2 SER 79...
...
/v GLU 452
/x MET 289

Using Amber 20 recommended default charges and atom types for standard residues
Traceback (most recent call last):
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275, in execute
    cmd.run(cmd_text)
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
    result = ci.function(session, **kw_args)
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
    assign_charges(session, needs_assignment, his_scheme, charge_method,
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges
    add_charges(session, charged_residues, method=charge_method, status=status)
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 19, in add_charges
    uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user,
  File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges
    for res_type, residues in uncharged_res_types.items():
RuntimeError: dictionary changed size during iteration

RuntimeError: dictionary changed size during iteration

File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges
for res_type, residues in uncharged_res_types.items():

See log for complete Python traceback.

Thanks
Yaikhomba

________________________________
From: Y. Mutum <ym337 at cam.ac.uk>
Sent: 14 February 2021 11:02
To: Tom Goddard <goddard at sonic.net>
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 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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