AMBER Archive (2009)

Subject: Re: [AMBER] problem in rmsd

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Tue Mar 10 2009 - 03:30:16 CDT

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
representations.

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