VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Feb 02 2008 - 15:30:18 CST

Hi,
  I'd actually suggest using "mol ssrecalc" rather than "mol reanalyze",
as the ssrecalc only recalcs secondary structure, whereas the reanalyze
command causes _everything_ in the structure to be re-analyzed from scratch.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 02, 2008 at 08:42:40AM -0600, Peter Freddolino wrote:
> Hi Aneesh,
> to calculate the secondary structure for a selection at a given
> timestep, you should got to that timestep, and the use the command
> mol reanalyze top
> which runs that timestep through stride (among other things). Once this
> is done, you can access the secondary structure of an atomselect object with
> $sel get structure
>
> This will return a string with a one letter description of the secondary
> structure at each position in your atom selection (eg. 'H' for helix).
> You can then calculate %helicity by counting the Hs.
>
> Best,
> Peter
>
> aneesh cna wrote:
> >hello,
> > Alex,thank you for immediate reply.Is there any plug-in in VMD to
> >calculate % helicity ? or is there any script to do such calculation
> >?. Any help is appreciable
> >
> >with regards
> >Aneeh
> >
> >On Feb 1, 2008 11:07 AM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> ><mailto:akohlmey_at_cmm.chem.upenn.edu>> wrote:
> >
> > On Jan 31, 2008 11:54 PM, aneesh cna <aneeshcna_at_gmail.com
> > <mailto:aneeshcna_at_gmail.com>> wrote:
> > > Hello VMD users,
> > > Is it possible to calculate %helicity
> > over time
> > > using VMD ?.
> >
> > yes.
> >
> >
> > >
> > > Thanks in advance
> > > Aneesh
> > >
> >
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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