On 10/10/12 5:43 AM, Shima Arasteh wrote:
Hi,
I'm doing the protein insertion into the lipid membrane. After shrinking for 30
times, I visualized the system, but the secondary structure of protein is still
incomplete . How come? I finished the InflateGRO step.
Visualization oddities like these are a result of (1) distorted geometry of the
protein or (2) atomic overlap with other molecules that cause rendering
algorithms to fail. It should be very easy to identify what is going on based
on the magnitude of forces in EM and visual inspection of the areas with
"broken" secondary structure.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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