VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri May 27 2011 - 16:52:50 CDT

The cavity visualization tools I know about are for static structures - caver, castp, & surfnet implemented through Chimera. So there would be utility for an analogous VMD tool that could be coupled to trajectory animation, enabling convenient mapping of cavity size throughout a simulation w/out having to analyse n separate pdb snapshots, where n is limited by one's stomach for tedium & will undoubtedly be << the trajectory size.
 
Irene Newhouse
 
> Date: Fri, 27 May 2011 14:47:03 -0500
> From: johns_at_ks.uiuc.edu
> To: bvaldebenito09_at_alumnos.utalca.cl
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Protein cavities
>
>
> Hi,
> The DX files are a visualization file format that can also be used to store
> uniform grids of scalar data, which is what the 'volmap' commands do.
> If you compute a density map from your structure, you'll get density values
> of zero at the points associated with empty space, so that is a very simple
> way to determine where you have pockets or cavities of empty space.
> You could get a crude estimate of empty volume from this kind of approach,
> but I should also point out that with a little google searching, that
> I think that there are tools available that are specifically designed to
> find cavity volumes. So, before you implement it yourself in a VMD
> script, I would suggest googling for 15 or 20 minutes and see if you can
> find one of those tools. I seem to remember I've heard of a couple such
> programs in the past, but I don't remember them anymore.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
>
> On Thu, May 26, 2011 at 05:41:48PM +0000, BRAULIO FAVIN VALDEBENITO MATURANA wrote:
> > Dear all,
> >
> > We're working on a Tcl/Tk script whose function is to determine both
> > surface and internal cavities of a given protein. In order to achieve
> > that, we've been thinking in the "volmap" function as stated by John Stone
> > in reply to "cavity/pocket representation" on May 2nd, 2006 (it can be
> > seen here:
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6885.html), but
> > instead of a graphical output, we need the analytical data too.
> >
> > Well, regarding the output of the "volmap" command, which is a file with
> > .dx extension, we would like to know if there is any way to use the
> > information on that file so that we can "substract" from the entire map
> > the volume occupied by the actual molecule, thus letting the volume of any
> > possible cavities.
> >
> > Thanks in advance!
> > Braulio.
>
> --
> NIH Resource 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/ Fax: 217-244-6078