AW: secondary structure analysis

From: Norman Geist (
Date: Thu Jan 10 2013 - 00:16:07 CST

Hi Erik,

a nice tool doing that is ptraj part of the free ambertools. It can output
statistical information about the probability of selected resids to contain
to which secondary structure for a whole trajectory (or multiple). It works
for both amber and charmm.

Regarding VMD (this is the NAMD mailing list btw), as far as I know, the
STRIDE program is called externally on a pdb file that was written
temporarily by VMD and will result in cryptically named file, usually in the
/tmp folder (but there's an environment variable like VMD_TMP or something
like that). Maybe check this files. Also, VMD will call STRIDE only _1_ time
at first usage of coloring method "secondary structure" or representation
"[new] cartoon" or "[new] ribbons" and only for the currently active frame.
So to get the secondary structure refreshed every frame, you are maybe
interested in the sscache.tcl file which is downloadable in the net. You can
source this file into VMD via console and simply do "start_sscache". This
will cause the secondary structure to be cached for every frame (1st play of
the frames will be slower), what should IMHO be part of VMD anyway as
everything else is pretty dangerous.

No idea about the timeline tool (never used) but maybe you can easily
transform the data with a little script.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Martin, Erik W
> Gesendet: Mittwoch, 9. Januar 2013 21:21
> An:
> Betreff: namd-l: secondary structure analysis
> Hi, I'm wanting to loop through my trajectories and find out if a
> particular residue is predicted to be in a particular type of secondary
> structure in each frame.
> I know that stride computes this data, but I'm not sure where its
> stored, or how to access it in a script. Also, I know that in VMD I
> can use the "timeline" tool, but the way it writes out data isn't
> particularly friendly for making additional figures.
> Has anyone done something like this before?
> Thanks, Erik
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