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]
?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@cgl.ucsf.edu> on behalf of Y. Mutum <ym337@cam.ac.uk> Sent: Tuesday, May 18, 2021 4:47 PM To: chimerax-users@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]
Hi, Although both the Segment Map and the Measure Color and Blobs tools have been added to ChimeraX (Segment Map added July 2019, Measure and Color Blobs in May 2019), that approach may not be what you had in mind, because it would make separate segmentation surfaces. Also it may be hard to get the areas of interest to segment separately... and if you were going to make two separate surfaces anyway, probably the split by color zone approach you already mentioned would be much easier. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html> The ChimeraX change log shows the approximate dates that features were added: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> If I understand Yaikhomba's question correctly, he just wants to measure the surface areas of different colors in a single isosurface. However, I don't know of a way, or at least I haven't thought of how to do it, in either Chimera or ChimeraX. (Other than writing some kind of python script, which I don't know how to do either.) If I think of a way, will let you know. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 18, 2021, at 2:06 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
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@cgl.ucsf.edu> on behalf of Y. Mutum <ym337@cam.ac.uk> Sent: Tuesday, May 18, 2021 4:47 PM To: chimerax-users@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
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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@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@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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@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@cam.ac.uk <mailto:ym337@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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Hi Tom, Elaine and Reza Thanks for the suggestions - I will try these and get back. Thanks Yaikhomba ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: 19 May 2021 02:32 To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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. [cid:FB0DA37D-E31F-40B5-BB24-3E49C4972D01] On May 18, 2021, at 2:35 PM, Tom Goddard <goddard@sonic.net<mailto:goddard@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@cam.ac.uk<mailto:ym337@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 [cid:71184965-9ba5-4374-82b3-bd2b264b4b0c] _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@sonic.net> Sent: 19 May 2021 02:32 To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@sonic.net <mailto:goddard@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@cam.ac.uk <mailto:ym337@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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participants (4)
-
Elaine Meng -
Reza Khayat -
Tom Goddard -
Y. Mutum