Thanks Robert for the reply,
A:I Have a 5 ns trajectory, saving data every 100 ps(50 frames).
A:NO, I just load the .pdb file of the trajectory and in console I
type "calculate structure" , it calculates for every frame of the trajectory
, but I don't know How I can save it which be useful for plotting.
because I want a plot like the DSSP plot which people use in literatures.
________________________________
From: Robert Hanson <[email protected]>
To: parisa rahmani <[email protected]>; "[email protected]"
<[email protected]>
Sent: Wednesday, January 2, 2013 4:44 PM
Subject: Re: [Jmol-users] trajectory + secondary structure analyze
Q: How many trajectory frames do you have?
Q: Are you using "load TRAJECTORY ...." ?
If your intent is to see how the secondary structure changes from frame to
frame, then on each frame change you will need to calculate a structure using:
set animFrameCallback "jmolscript:calculate structure;cartoons only;color
structure"
or something like that. Otherwise the assignments for helix, sheet, and turn
will not be updated automatically.
On Tue, Jan 1, 2013 at 1:53 AM, parisa rahmani <[email protected]> wrote:
Hi jmol users
>
>
>I am new to jmol, and unfamiliar with it's facilities.
>
>
>I have a trajectory of a protein(.pdb file) and i want to plot a graph to show
>changes in secondary structure as a function of time,
>i know that with "calculate structure" i can do DSSP analyze, but how i can
>save it such that i can plot the graph.
>
>any suggestion (or introducing some tutorials) would be greatly appreciated.
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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