Re: [AMBER] problem in rmsd

From: Hannes Loeffler <>
Date: Tue, 10 Mar 2009 08:30:16 +0000

On Mon, 2009-03-09 at 23:36 -0400, Parimal Kar wrote:
> I output PDB files for each frame. interesting thing is when I
> choose the option "new cartoon" in vmd, then the figure disappears.

I think vmd computes the secondary structure (via the stride program)
only once. I am not sure on what frame it operates (first?, last?). It
happened to me occasionally that vmd gets totally confused and wasn't
able to display parts or all of a structure anymore. My advice would be
not to rely 100% on vmd when you use "new cartoon", "tube" or similar

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Received on Wed Mar 11 2009 - 01:21:09 PDT
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