Re: [Jmol-users] trajectory + secondary structure analyze

[parisa r. <ra...@ya...>]

http://www.google.com/imgres?um=1&hl=en&client=ubuntu&sa=N&tbo=d&channel=fs&biw=1138&bih=500&tbm=isch&tbnid=rW-wtAYDRZ5fRM:&imgrefurl=http://www.sciencedirect.com/science/article/pii/S0006349502751539&docid=3sBXVhElLhW3pM&imgurl=http://ars.els-cdn.com/content/image/1-s2.0-S0006349502751539-gr7.jpg&w=553&h=441&ei=JGPlUNCuAquN4gS0sIAQ&zoom=1

in above webpage, there is a example of plot.



________________________________
 From: Robert Hanson <ha...@st...>
To: parisa rahmani <ra...@ya...> 
Cc: "jmo...@li..." <jmo...@li...> 
Sent: Thursday, January 3, 2013 2:16 PM
Subject: Re: [Jmol-users] trajectory + secondary structure analyze
 

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 <ra...@ya...> 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 <ha...@st...>
>To: parisa rahmani <ra...@ya...>; "jmo...@li..." <jmo...@li...> 
>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 <ra...@ya...> 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