[Chimera-users] Average slab thickness

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


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.


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   

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