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

[Reza Khayat]

?Hi,


Not sure if this is possible in ChimeraX yet but can do this in Chimera. Use map segmentation to separate green from grey. Then use surface measure tool (Mesure and color Blobs) to measure the surface area.


Best wishes,
Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Y. Mutum <ym337 at cam.ac.uk>
Sent: Tuesday, May 18, 2021 4:47 PM
To: chimerax-users at cgl.ucsf.edu
Subject: [EXTERNAL] [chimerax-users] Measuring surface area of a colored portion of the map

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

[cid:71184965-9ba5-4374-82b3-bd2b264b4b0c]
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