[chimerax-users] Measuring surface area of a colored portion of the map

[Tom Goddard]

Hi Yaikhomba,

  Why do you want surface area instead of volume?  Volume seems more sensible as it would be very closely related to the number of modeled and unmodeled atoms.  Also volume is easy to get using command "volume splitbyzone" and "measure volume".

  If you have a good reason for wanting surface area it would not be very hard to do it with some Python code if you ignore the triangles of the surface that have a mix of green and gray vertex colors.  I can provide that Python code if you give a good reason why surface area is better than volume.

	Tom




> On May 18, 2021, at 1:47 PM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> 
> Hi
> 
> This problem relates to surface area of a low-resolution EM map using ChimeraX
> 
> I have opened the following map and the corresponding model using the following commands in ChimeraX. 
> 
> >>> open 4uq8; open 2676 from emdb
> >>> color #1 green; color zone #2 near #1 dist 4
> 
> As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area.  This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using the model.
> 
> Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of 'outer pixels of a map' that are colored green or gray, at a given map contour? 
> 
> Could you please help with a way to measure this without using the 'volume splitbyzone' command?
> 
> Thanks
> Yaikhomba
> 
> 
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