VMD-L Mailing List
From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Jul 29 2015 - 23:05:58 CDT
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Hi John,
Unfortunately no. We are not just at performance but we are in need of the
functionality. Currently we are investigating using measure contact $sel1
$sel2 while the selections are CA atoms of the residues. However we think
it cannot reflect the true story due to different geometrical sizes of the
side chains (i.e. residues with a large side chain might touch another
residue more frequently even if their CA atoms are relatively far apart).
In this case, we think if we can use com of the residue, it might be more
accurate.
Thanks,
Kevin
On Wed, Jul 29, 2015 at 12:22 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> This isn't a functionality of the existing code, but it could be added
> if enough people thought it would be useful. Is the goal just to
> increase performance, or to reduce the matrix size?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jul 27, 2015 at 02:16:45PM +0800, Kevin Chan wrote:
> > Dear Users,
> >
> > I'm wondering whether it is possible to make "measure contact" codes
> > return results according to centre of mass of the lists of residues
> of the
> > protein?
> >
> > Thanks in advance,
> >
> > Kevin Chan
> > Department of Physics and Materials Science
> > City University of Hong Kong
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
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