OK, so that's pretty easy:
load xxx.pdb
calculate structure
cartoons only;color structure // perhaps
Sounds like you are doing all that already.
Q: "save it for plotting" ? Meaning what exactly? Can you show me an
example of a "DSSP plot"?
Bob
On Thu, Jan 3, 2013 at 2:31 AM, parisa rahmani <[email protected]> wrote:
> 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
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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