Hi Alina, Sorry, Chimera does not calculate surface charge density. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 1, 2012, at 9:04 AM, IONEL , ALINA ELENA 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

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 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,

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@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

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