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

[Elaine Meng]

Hi Yaikhomba,
It is not simple to add charge calculations for nonstandard residues, and we have been working on it for months.  In fact, an initial version of this capability is available in the "coulombic" command in the ChimeraX mac version current daily build, but is not documented yet, and needs to be better tested and probably improved before it is ready for wider use.

*** More importantly: I do not think it is reasonable to do electrostatics calculations on this huge structure, not because of its size per se, but because as the Log messages are telling you, it is missing atoms from many dozens of STANDARD residues, i.e., their side chains were not built or were only partially built.  Probably the atom positions could not be resolved by the authors from the density map at this resolution. ***

Obviously if lots of charged residues are missing their side chains, their charges will not be represented and it will be fairly meaningless to calculate an electrostatic potential from the remaining atoms, or to try to draw any conclusions from what you get.  It is important to pay attention to these Log messages telling you that there are atoms missing.

Finally if you believe there is a bug causing a traceback, please use the "report a bug" dialog (e.g. from the Help menu, or sometimes the error dialog has a button to open it directly) rather than sending e-mail to this list.

I hope this clarifies the situation,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Feb 14, 2021, at 5:06 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> 
> 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
> 
> Get Outlook for Android
> 
> 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> 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