VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Tue Dec 11 2001 - 11:46:33 CST

Hi Noklai,

On Tue, Dec 11, 2001 at 02:45:20PM +0100, Nikolai Smolin wrote:
> Dear VMD users!
>
> Somebody knows how possible calculated percentage
> of helical and sheet structure of proteins throw MD-trajectory?
> What programs can do this or it possible by VMD?

        It sounds like you want to

        1. recalculate secondary structure at every frame of a trajectory.
        2. Count the residues in each frame that are helical, sheet,
or other.
        
        
        This can be done in vmd with a little tcl scripting.

        Step 1.
        Run the script in:
         http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/

          This script calculates secondary structure for the frames in
a loaded trajectory, then changes the structure appropriately as you
move through the trajectory with the Animate window or 'animate' commands.

        Step 2. When the structure has been calculated for a frame,
go that frame, then get a list of sec. structure with:
                 set sel [atomselect 0 "protein and name CA"]
                 set structList [$sel get structure]

        So structList is set to..
C C C C C E E E E E E E T T T T C C E E E E E E C C C T T T T C E E E E E E E E T T T T C C C C E E E E E T T T T C E E E E T T T T T T T C E E E E E E E E E T T E E C C C E E E E E
...you get the idea.

                Now you can go through structList, count residue
structures, and get your statistics. To compare frames, just loop
over this and keep track of the data as you step through frames.
Thanks for using VMD!

                                        Cheers,

                                        Barry
                 
        

>
> Thanks in advance!
>
> --
> Nikolai Smolin
>
> Physikalische Chemie I
> Universit?t Dortmund
> Otto-Hahn-Str. 6
> 44221 Dortmund
> Germany
>
> Fax: +49 / 231 / 755 3901
> E-mail: smolin_at_steak.chemie.uni-dortmund.de
> 

-- 
Barry Isralewitz     Beckman 3121    Theoretical Biophysics Group, UIUC  
Office Phone: (217) 244-1612    Home Phone: (217) 337-6364
email: barryi_at_ks.uiuc.edu      http://www.ks.uiuc.edu/~barryi