Visualization of protein aqueous solution
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
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.htm...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...> Of course, you could also do that by just text-editing your PDB file. Best, 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 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
Hi Nikolay, One more idea: since this is just for display, you could use "Volume Tracer" to place "markers" (which are essentially fake atoms) interactively in space. Although it is called volume tracer, you can place markers in space independent of any volume data. menu: Tools... Volume Data... Volume Tracer in that dialog's Mouse menu, turn off all settings except turn on "Place markers outside data" ... then proceed to place markers interactively. You can move them around, change radii and color, etc. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/fr...> Elaine On Sep 10, 2012, at 2:42 PM, Elaine Meng wrote:
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.htm...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.htm...>
Of course, you could also do that by just text-editing your PDB file. Best, 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 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
On Sep 10, 2012, at 2:06 PM, Nikolay Igorovich Rodionov wrote:
I've tried using add-ion but I haven't had good results.
So what was the problem with the results? The results seem good to me if I add a specific number of ions (depends on the system; in the attached image: 50). If you add ions to neutralize the charge you will get a relatively small number clustered around the solute rather than a larger number spaced throughout the solution. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Nikolay Igorovich Rodionov