[Chimera-users] Average slab thickness

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 19 10:48:05 PDT 2008

Hi Jeff,

  The Chimera mask command code can be adapted to calculate the average 
thickness of a slab defined by two surfaces.  I've attached the adapted 
Python code.  You select the surfaces then open the script and it 
reports the mean thickness, standard deviation of thickness, min/max 
thickness and number of thickness samples used.  The script contains a 
projection axis which should be perpendicular to the slab and a grid 
step which defines the grid spacing.  The thickness is measured on a 
grid perpendicular to the axis and only grid points where the projection 
axis intersects the surfaces at least twice are used.  You have to edit 
the script (at the bottom) to set the projection axis and grid step to 
appropriate values.  Those values could be automatically set using the 
Python code of the inertia ellipsoid script I gave you earlier.  Tested 
in Chimera version 1.2498 on a spherical surface.


Jeff wrote:
> hi Tom,
> I'd like to compute the 'average distance' between two surfaces to 
> calculate the width of a cellular compartment (have attached an image, 
> the two surfaces delineating the compartment are colored blue).
> one way that has been suggested to me is to calculate the volume 
> between the two surfaces, and then just divide by a mean path length 
> along one of the surfaces. I know that chimera has a volume 
> calculation tool for an isosurface, and was wondering if I could use 
> the surfaces you see to do a volume calculation (and, if so, how I 
> would go about capping those surfaces to create a closed surface). If 
> able to calculate the volume that way, I could just use the path 
> length of a contour (which I have) that generated one of the two 
> surfaces to derive the "average width".

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