# [Chimera-users] Surface charge density!

Tom Goddard goddard at sonic.net
Mon Mar 5 16:32:56 PST 2012

Hi Alina,

I don't understand what you want.  Here are a few Chimera tools that

Menu Actions / Surface / show.  This will make the surface and report

charges to atoms.  It will allow you to add hydrogens if your structure
does not have them, a necessary step for determining charges.

Chimera select command to select atoms which have at least 1 square
Angstrom of solvent accessible area:

sel #0@/areaSAS>1

Menu Tools / Structure Analysis / Attribute Calculator.  This will
let you sum the charges on the selected atoms.  Switch it to attribute
for "molecules", use formula

sum(atom.charge)

and turn on the switch "Restrict formula domain to current selection"
and press Apply.

The above tools allow you to compute the total charge near divided by
the total surface area. That seems like a worthless number.  But maybe
you have in mind some related quantity that is useful for your work and
this will get you started.

Tom

> Hi Tom,
>
> and, told me that chimera don´t calculate surface charge density.
> In this case if is possible to calculate how you write me, the local
> charge density will be good. If not, only approximately, how can
> express Kcal/mol*e en Coulomb?
>
> Thanks, Alina
>
>
>
> Quoting Tom Goddard:
>
>> Hi Alina,
>>
>>   By surface charge density do you mean the total charge on surface
>> residues divided by the total surface area?  Or do you want local
>> charge density, like just the outside face of the capsid?  Those
>> could probably computed in Chimera. How will you use this value?
>>
>>   Tom
>>
>>
>> On Mar 1, 2012, at 9:04 AM, "IONEL , ALINA ELENA"
>> <aionel at cnb.csic.es> wrote:
>>
>>> Hi,
>>>
>>> My name is Alina Ionel and I am PhD student. I have a pseudoatomic
>>> model (in pdb format) for a capsid protein. I did a representation
>>> of the electrostatic potential in Chimera with the option “Coulombic
>>> Surface Coloring” for a hexamer, for example. The unit of this
>>> potential are in Kcal/mol*e and the surface is colored in a range of
>>> values -10 to 10 Kcal/mol*e.
>>> I want to know the surface charge density for this hexamer (in
>>> C/m2). I need the value.
>>> Can you help me, please?
>>>
>>> Thank you, Alina
>>>
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>
>
>