On Fri, Feb 5, 2016 at 12:44 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
wrote:
> Hi Carlos,
> Thank you for responding.
> I know this seems like a silly question, but how can I tell whether the
> protein interacts with its periodic images?
>
Look at an imaged snapshot where the protein is at the center of the unit
cell. Is the protein close to the edge of the unit cell in any of the
dimensions?
With VMD, you can also visualize multiple unit cells (in the
representations pane). Then you can see quite clearly how close two
periodic images are to one another and whether their dynamics seems to
indicate they are interacting. (Basically what you're looking for are
correlated motions on opposite sides of the protein that appear to arise
through inter-image interactions.)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 05 2016 - 11:00:04 PST
