[Chimera-users] Visualization of protein aqueous solution

[Elaine Meng]

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.  
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

Of course, you could also do that by just text-editing your PDB file.
Best,
Elaine
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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