[gmx-users] packing lipids
jalemkul at vt.edu
Mon Sep 24 16:50:37 CEST 2012
On 9/24/12 10:48 AM, Shima Arasteh wrote:
> In fact, the structure visualized by VMD and choosing line as draw style is ok, but the second structure of protein ( I mean the choosing ribbons) shows a broken structure. How come? what does it mean?
This is really more of a VMD question (there's a mailing list for that), but
I'll take a shot anyway. Broken ribbons sometimes result from other nearby
atoms getting in the way. That is, VMD detects "bonds" based simply on a
distance search, and sometimes it guesses wrong or sometimes there's something
legitimately wrong with your structure. It could simply be that there is a
lipid atom somewhat near a protein backbone atom and it is causing the rendering
algorithm to fail.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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