VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Dec 11 2007 - 11:18:14 CST

Hi Peter,

Thank you for the prompt suggestion. Perhaps I wasn't clear enough,
but basically what I want to get is an average % of helical content
per residue over time (i.e., a graph of % helical content vs residue).
The suggestion you gave me solves the problem if you want to get the
total helical content of the protein. So I wonder if it'll be
possible to do that with simple tcl scripting in VMD (I hope so!).

Thanks!
Michel

On Dec 11, 2007 5:39 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Michel,
> I'd recommend instead making a selection with the CA atoms of all the
> residues you're interested in, and then after going to each frame do
>
> mol reanalyze $mol
> set mystruct [$sel get structure]
>
> You can then parse the returned list for the number of "H" entries.
> Best,
> Peter
>
>
> L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> > I'm calculating the percentage of helical content of a protein (using
> > a NAMD-generated trajectory). I've been using the following script:
> >
> > set outfile [open protein_SS_16.txt w]
> > set numframes [molinfo top get numframes]
> > set sel [atomselect top "resid 16 and name CA"]
> > for {set frame 0} {$frame < $numframes} {incr frame} {
> > animate goto $frame
> > display update ui
> > vmd_calculate_structure top
> > $sel frame $frame
> > $sel update
> > set helixlist [$sel get alpha_helix]
> > set helixcount 0
> > puts $outfile " Alpha helix count: $helixcount "
> > }
> > close $outfile
> >
> > However, the script calculates the content *ONLY* for one residue at a
> > time, so I was wondering if you have any ideas on how to modify it so
> > I can get a table of residue vs count of alpha helix, or something
> > similar. This is basically to avoid calculating it for every residue
> > (which will take forever!). If you have alternative ideas, I'd be more
> > than happy to read them.
> >
> > Thanks!
> > Michel
> >
>