[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 
could help you compute total charge near the surface.

   Menu Actions / Surface / show.  This will make the surface and report 
total surface area in the reply log (menu Favorites / Reply Log).

   Menu Tools /  Structure Analysis / Add Charge.  This will assign 
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


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.


> Hi Tom,
> Thank you very much for your answer. Your colleague Elaine write me 
> 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
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