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@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.

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Date: Wed, 14 Oct 2009 13:54:03 -0700 From: goddard To: Sudheer CC: chimera-users@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

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Hi,

Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera?

Thank you, Sudheer Molugu.

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