[gmx-users] packing lipids

[Justin Lemkul]

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

-- 
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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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