[Chimera-users] Solvent Channel Dimensions

Damien Larivière damien.lariviere at fourmentinguilbert.org
Thu Sep 12 08:47:45 PDT 2013

Hi Matt,

Have you tried MOLE (http://webchem.ncbr.muni.cz/Platform/App/Mole)? I 
used it by the past to do something similar to what you want to do, it 
looked promising.

Best, Damien

Le 11/09/2013 00:41, Elaine Meng a écrit :
> Hi Matt,
> If you just need a linear distance (as opposed to something like cross-sectional area), probably the simplest way would be to place "markers" (basically fake atoms) on the surface at the desired locations with the mouse, then measure the distance between two markers.
> To place markers: choose menu: Tools.. Volume Data… Volume Tracer, and then in its Mouse menu make sure to uncheck all the choices except "place markers on surfaces."  There is also a setting for which mouse button will be used to do this.  Then you can add whatever markers you want on the surface.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
> To measure marker-marker distance:  these are fake atoms, so the same methods used to add a distance monitor can be used.  For example, Ctrl-click one, Shift-Ctrl-doubleclick the second to get context menu, choose "Show Distance."  Or, select two markers and then use command "distance sel" (etc.)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
> Cross-sectional area is discussed in this previous post.
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-June/007681.html>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 10, 2013, at 1:46 PM, "Thompson, Matthew K" <matthew.k.thompson at vanderbilt.edu> wrote:
>> How can I measure the dimensions of a solvent channel in a protein?  The channel is clearly visible after the surface in generated.  In addition, the cavity can be created with Surfnet.  Something like "Measure and Color Blobs" does not give the dimensions I need.  I am interested in the width of the channel at its most narrow point.
>> Thanks
>> Matt
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