[Chimera-users] Visualization of protein aqueous solution

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 10 14:42:30 PDT 2012

Hi Nikolay,
Other than Add Ions, the only other thing I can think of is to manually add atoms one by one at the desired x,y,z coordinates, which can be done with Build Structure, the "Start Structure" section.  

Of course, you could also do that by just text-editing your PDB file.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 10, 2012, at 2:06 PM, Nikolay Igorovich Rodionov wrote:

> Hi all,
> Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. 
> I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. 
> Much Thanks!
> Nikolay Rodionov

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