[Chimera-users] Hydrodynamic radius

[Tom Goddard]

Hi Sudheer,

  I don't know if the theoretical hydrodynamic radius Rhyd defined on 
the wikipedia page

    http://en.wikipedia.org/wiki/Hydrodynamic_radius

is a good approximation to the Stokes' radius.  The Stokes' radius 
depends on both shape and hydration details.

  I've added a request for this calculation in Chimera to our feature 
request page (item 220).

    http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests

This is much more specialized than typical Chimera features and I would 
not expect it to be implemented any time soon.  If you wished to 
implement it I could probably show you how to get out of Chimera a list 
of grid points within a displayed contour level that would be the input 
to the calculation.

  Tom

-------- Original Message --------
Subject: Re: [Chimera-users] Hydrodynamic radius
From: Sudheer
To: goddard at cgl.ucsf.edu
Date: 10/14/09 2:03 PM
> Hi Tom,
>
> Im interested in the optical properties of a protein. Yes, "the 
> hydrodynamic radius for a uniform solid bounded by a contour surface 
> of your map would be useful". Yes, Stocks radius. Actually I'm running 
> Dynamic light Scattering experiment to find the variation in the size 
> distribution of a protein with change in Temperature. (I mean im 
> trying to find at what temperature the protein forms monomer and 
> dimer...!) I already have Cryo-EM map of the dimer and so just thought 
> of comparing the Hydrodynamic radius between the cryo-map and the DLS 
> result.
>
> I hope you got my interest in finding the Hydrodynamic radius of my 
> protein.
>
> Thank you very much for your help,
> Sudheer.
>
> > Date: Wed, 14 Oct 2009 13:54:03 -0700
> > From: goddard
> > To: Sudheer
> > CC: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Hydrodynamic radius
> >
> > Hi Sudheer,
> >
> > Chimera isn't able to compute hydrodynamic radius of maps or
> > molecules. Are you primarily interested in diffusion properties or
> > optical properties of your structure? Do you think the hydrodynamic
> > radius for a uniform solid bounded by a contour surface of your map
> > would be useful? Do you mean Stokes' radius or the R_H defined on the
> > wikipedia page?
> >
> > http://en.wikipedia.org/wiki/Hydrodynamic_radius
> >
> > The latter looks like a pretty simple calculation.
> >
> > Tom
> >
> > -------- Original Message --------
> > Subject: [Chimera-users] Hydrodynamic radius
> > From: Sudheer
> > To: chimera users
> > Date: 10/14/09 1:05 PM
> > > Hi,
> > >
> > > Can I measure the Hydrodynamic radius a Cryo-EM density map using 
> Chimera?
> > >
> > > Thank you,
> > > Sudheer Molugu.
> > > 
> ------------------------------------------------------------------------