Selecting atoms outside (or inside) a density map's contour
Dear ChimeraX Team,
I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them.
I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera.
What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour.
In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX.
I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well.
I will appreciate any tips and suggestions!
Kind regards, Mateusz
Dear Mateusz, Thanks for your kind words!
You can do it in ChimeraX by assigning the atoms the map values (at their positions) as attributes, and then using the attribute value as selector. For example, if the atoms are in #1 and the map is #2 and the contour level is 0.035:
measure mapvalues #2 atoms #1 attribute mvalue sel @@mvalue<0.035
As you can see, this does not depend on showing a contour surface. You could give any value in the selection by attribute value, and you could use symbols for greater than, less than, greater than or equal to, etc.
See: https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#mapvalues https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 21, 2022, at 8:17 AM, Mateusz Dobrychłop via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Team,
I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them.
I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera.
What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour.
In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX.
I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well.
I will appreciate any tips and suggestions!
Kind regards, Mateusz
Dear Elaine,
Perfrect, thank you. This works like charm.
Kind regards, Mateusz ________________________________ Od: Elaine Meng meng@cgl.ucsf.edu Wysłane: czwartek, 21 kwietnia 2022 17:53 Do: Mateusz Dobrychłop mdobrychlop@amu.edu.pl DW: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Temat: Re: [chimerax-users] Selecting atoms outside (or inside) a density map's contour
Dear Mateusz, Thanks for your kind words!
You can do it in ChimeraX by assigning the atoms the map values (at their positions) as attributes, and then using the attribute value as selector. For example, if the atoms are in #1 and the map is #2 and the contour level is 0.035:
measure mapvalues #2 atoms #1 attribute mvalue sel @@mvalue<0.035
As you can see, this does not depend on showing a contour surface. You could give any value in the selection by attribute value, and you could use symbols for greater than, less than, greater than or equal to, etc.
See: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmeasure.html%23mapvalues&data=05%7C01%7Cmdobrychlop%40amu.edu.pl%7C1ed6f5a481f848132cb508da23af18dc%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637861532874496379%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=P%2BKS7AtLm8wopfuPl4vR09OJMqCmz1M%2FIVD9kZUbhEY%3D&reserved=0 https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fatomspec.html%23attributes&data=05%7C01%7Cmdobrychlop%40amu.edu.pl%7C1ed6f5a481f848132cb508da23af18dc%7C73689ee1b42f4e25a5f666d1f29bc092%7C0%7C0%7C637861532874496379%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I7YB6p1%2FdJw5zlUYbmdOwrEItviJnW%2F6A%2FvKQurKS0o%3D&reserved=0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 21, 2022, at 8:17 AM, Mateusz Dobrychłop via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Team,
I'm a structural bioinformatician working on my PhD thesis. I've been a long time user of Chimera, and I'm now using ChimeraX to create figures for my dissertation. I genuinely love both programs. Thank you for creating them.
I found myself stuck trying to perform one operation in ChimeraX that is very easy to perform in Chimera.
What I'm trying to do is select (and color) all atoms of an atomic model, that are located outside of a density map's contour.
In Chimera, I was able to just select the model and use the shortcut "ac oa" and that was it. Unfortunately I am not able to find a way to do that in ChimeraX.
I even tried to select the atoms in Chimera, then save the selected atoms as a PDB file, and then the inverted selection as a separate PDB file, and then open the two files in ChimeraX and color them separately. This could even work for a full atom representation, but does not work well for ribbon representation. That said, if the solution to my problem could be to somehow transfer the list of atoms that are outside the map from Chimera to ChimeraX, that would work for me as well.
I will appreciate any tips and suggestions!
Kind regards, Mateusz
participants (2)
-
Elaine Meng -
Mateusz Dobrychłop