[chimerax-users] MLP value of the ASP and GLU carboxylate

[Tristan Croll]

To me, it looks like these values were calculated for the protonated 
forms of ASP and GLU. By convention, OD2 and OE2 are the atoms that 
receive the hydrogen.

On 2019-07-12 21:27, Zhijie Li wrote:
> Hi Elaine,
> 
> Thanks for the explanation. I understand the complications.  However
> this function directly affects a button in the GUI that a lot of user
> probably will press.  In Chimera it also controls a preset scenario?
> For membrane proteins it might not be a problem but for soluble
> proteins the outcome might be quite misleading. I think if the
> underlying parameters are highly questionable it is probably better
> not to make it so accessible to the users. Or maybe add a caveat note
> in the documents?  Just my opinions.
> 
> Regards,
> 
> Zhijie
> 
>> On Jul 12, 2019, at 11:46 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Zhijie,
>> We’ve also noticed the same issues with these atomic potentials.  
>> However, so far we have only implemented the MLP method based on pyMLP 
>> with these original values (developed by others), not wanting to get 
>> into the parametrization business ourselves.
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>
>> <https://github.com/plantigrade/pyMLP>
>> 
>> There may be different atomic potential sets for use with MLP that 
>> were already developed by others, but they would take time to add, so 
>> we haven’t thoroughly researched the issue.  If you have opinions or 
>> suggestions, let us know.
>> 
>> As an alternative, I’ve provided a ChimeraX command script to color 
>> protein surfaces by the Kyte-Doolittle hydropathy values of amino 
>> acids (like the preset that is available in Chimera).
>> <http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>
>> 
>> However, those Kyte-Doolittle values are simply a constant for each 
>> amino acid type, rather than a potential that varies in 3D space.  
>> Still I find that the two approaches (Kyte-Doolittle values vs. MLP) 
>> often give a very similar picture of a transmembrane protein.
>> 
>> You can add it as a custom preset in ChimeraX using the instructions 
>> here:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
>> 
>> It could be easily modified to any amino acid hydrophobicity scales, 
>> or you could have multiple presets for the different scales.  Several 
>> scales are shown in this table from the Chimera User Guide:
>> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Jul 11, 2019, at 9:48 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:
>>> 
>>> Hello,
>>> 
>>> I noticed that the lipophilic atomic potentials of OD2 and OE2 are 
>>> set to very positive values in mlp.py:
>>> 
>>> 'ASP': {'C': -0.54,
>>>         'CA': 0.02,
>>>         'CB': 0.45,
>>>         'CG': 0.54,
>>>         'N': -0.44,
>>>         'O': -0.68,
>>>         'OD1': -0.68,
>>>         'OD2': 0.53}
>>> 'GLU': {'C': -0.54,
>>>         'CA': 0.02,
>>>         'CB': 0.45,
>>>         'CD': -0.54,
>>>         'CG': 0.45,
>>>         'N': -0.44,
>>>         'O': -0.68,
>>>         'OE1': -0.68,
>>>         'OE2': 0.53},
>>> 
>>> As as result the hydrophobic surface representation always show 
>>> hydrophobic patchs on the carboxylates, which look quite odd to me.   
>>> Is there a justification for this setting?  In addition, aren't the 
>>> two oxygens in the carboxylate equal considerting that they are in 
>>> resonance?
>>> 
>>> Zhijie
>> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users