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

[Tom Goddard]

Hi Yaikhomba,

  The "surface splitbycolor" command did not make it into the ChimeraX daily build last night (May 19), it will be in the May 20 build.  Unfortunately I forgot to push the change to our source code repository yesterday.

	Tom


> On May 19, 2021, at 2:22 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> 
> Hi Tom, Elaine and Reza
> 
> Thanks for the suggestions - I will try these and get back.
> 
> Thanks
> Yaikhomba
> From: Tom Goddard <goddard at sonic.net>
> Sent: 19 May 2021 02:32
> To: Y. Mutum <ym337 at cam.ac.uk>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Measuring surface area of a colored portion of the map
>  
> Hi Yaikhomba,
>   
>   I added to ChimeraX a command "surface splitbycolor #3" to split a surface model into separate surfaces for each color of the original surface.  Then you can use "measure area #4.1" to measure surface area of different colored pieces.  The surfaces in ChimeraX are made up of triangles, and colors are only assigned to the 3 vertices.  Single color triangles (all 3 vertices have the same color) are put into separate surface models by color called "piece 1", "piece 2", ....  And triangles that are multicolored are put into a model called "multicolor".  Usually single color patches are separated by a thin line of multicolor triangles that bridge the two single colored regions.
> 
>   Thanks for sending me an explanation (private communication) of why you want to measure the surface area of colored patches. I don't fully understand it and I am not sure it will be useful, but you can try.  Will be in tonight's ChimeraX daily builds on the download web page.
> 
> Tom
> 
> Map surface at left split by color on right.  Then I used drag mouse mode to move some of the colored pieces.  Note the "multicolor" boundary line left where I moved away pieces.
> 
> 
>> On May 18, 2021, at 2:35 PM, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> 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 <mailto: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
>>> 
>>> 
>>> _______________________________________________
>>> ChimeraX-users mailing list
>>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>>> Manage subscription:
>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210519/50b0b38f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image1.png
Type: image/png
Size: 613117 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210519/50b0b38f/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 724538 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210519/50b0b38f/attachment-0003.png>