# [Chimera-users] Average slab thickness

William Jeffrey Triffo triffo at rice.edu
Wed Mar 19 11:01:00 PDT 2008

```Tom,

much thanks!

I have a (goofy) movie I made from some of my data, that shows what I
was using your surface masking tools for. I can send it to you if you
want to take a look; be forewarned that I am not much of a visual artist.

-Jeff

Tom Goddard wrote:
> 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.
>
>    Tom
>
>
>
> 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".
>>
>

--
-------------------------------------------------------------
Jeff Triffo
Auer Group, Donner Lab, Lawrence Berkeley National Laboratory
Raphael Group, Bioengineering Department, Rice University
Medical Scientist Training Program (MSTP), Baylor College of Medicine
phone (Berkeley): 510-486-7940
fax   (Berkeley): 510-486-6488

```