[Chimera-users] fill solvent accessible channels

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 16 17:09:30 PST 2021

Hi Dieter,
There's no "fill cavities" tool. I was trying to think of some clever way to do it with a mask, but even if you had the void space filled and vice versa, it doesn't seem to simplify checking size selectivity.  As far as I know, you would still need to place a couple of markers across from each other where there seems to be a constriction and measure the distance between them.  That would be tedious and highly dependent on your skills at placing markers.

Maybe other people have ideas, or suggestions of other programs that might be useful.

As you probably know, most of the channel analysis tools work on atomic structures (.... Hole, MoleOnline, Caver, 3V, MolAxis...). 

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 16, 2021, at 1:10 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Hi,
>     I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity.
> Thanks, best, Dieter

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