[Chimera-users] Calculation of the average isoelectric point of a proteins solvation shell

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 20 08:09:13 PST 2015

Dear Csaba Nagy,
Sorry no, there is no such calculation in Chimera.  You could only get the net charge of the system after using Add Charge (in menu under Tools… Structure Editing).  It will ask you to add hydrogens first if you don’t already have them. The net charge would be reported in the Reply Log (open from Favorites menu).  If the solvation shell is only water they will all be considered to have formal charge of zero, so the system will have the same net charge as the protein alone.


Best regards,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 20, 2015, at 5:37 AM, Csaba Nagy <csaba.nagy at utu.fi> wrote:
> Dear Chimera Developers and -Users,
> I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range.
> I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful.
> Could you tell me please, if there is any option to make this estimation in Chimera?
> Thank you very much in advance!
> Best regards,
> Csaba Nagy

More information about the Chimera-users mailing list