VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 02 2012 - 00:00:15 CST

Joe,
  There may even be an existing "coloring by RMSD" example script
floating around somewhere that you could use or modify for your purpose
if you search the VMD-L mailing list archive. I've attached a (very old)
per-residue RMSD script in case you don't find a better one searching
the mailing list.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 02, 2012 at 12:49:19AM -0500, Joseph Bylund wrote:
> John,
> Thanks a bunch for answering two questions in one day (I had almost
> forgotten about that previous one). Hopefully I'll have a chance to
> investigate both of these in more depth later.
> -Joe
>
> On 02/02/2012 12:14 AM, John Stone wrote:
> >Joe,
> > This could certainly be done. You would just need to measure
> >the RMSD values for each residue, and then store the results into
> >one of the available per-atom data fields for each atom in the residue
> >(e.g. use a "same residue as ...." type atom selection.)
> >Once the data has been stored, you can use the field you've loaded the
> >RMSD values into as the coloring method in VMD. For a time-varying
> >property,
> >like RMSD or RMSF you'll want to use one of the four "user" fields, since
> >they are stored per-atom, for each frame.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Fri, Jan 06, 2012 at 12:40:27PM -0500, Joseph Bylund wrote:
> >>I'm interested in coloring each residue in a trajectory by its RMSD to
> >>its initial location. Similar to here:
> >>http://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/node5.html
> >>(except rmsd instead of qres), but using frames of a trajectory instead of
> >>aligned structures. Is there a way to do this?
> >>thanks for any help,
> >>-Joe
>
>
> --
> Joseph Bylund
> February 2, 2012
> Strength does not come from physical capacity. It comes from an indomitable
> will.
> Mahatma Gandhi 

-- 
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