Hi Yoseph, If you know how to program in Python, here is example ChimeraX Python code that places markers on all the connected surface pieces, and this might be something you could modify to show only a surface piece closest to a marker. https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html Tom
On May 17, 2024, at 4:57 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Yoseph,
So you have a volume and you have markers shown in ChimeraX and you wanted to show only the connected surface piece from the volume contour surface that is closest to a specific marker? Do I have that right? You show in your image a lot of markers, but you only want to find the surface piece close to one of them? And you just want to show it and hide all the other parts of the surface? What if the closest surface piece is far away? Or what if a tiny spec of surface is close, but a bigger surface piece is nearby?
I think that would require writing some Python code. There is nothing in ChimeraX that I can think of that computes connected surface pieces that are close to a marker.
Did you consider just showing a zone of the surface around the marker out to a certain specified distance? The ChimeraX surface zone command does that, described here
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/surface.html#zone
Tom
On May 17, 2024, at 4:05 PM, Yoseph Loyd <yoseph.loyd@mines.sdsmt.edu> wrote:
Hi Tom,
Sorry I was having a difficult time uploading an example image to the form. I'll attach it below, I'm displaying tracked centroids as small spheres. I was hoping that there existed a way to display the nearest yellow blob to the tracks I care about. The yellow blobs signal wise are full binary objects. Thank you for helping me with this.
Best, Yoseph
On Fri, May 17, 2024 at 4:43 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Yoseph,
I don't know what you mean "objects that fit to a centroid that I've tracked". What kind of object? The centroid of what? And why isn't it displayed currently? You'll have to explain better.
Tom
On May 17, 2024, at 2:07 PM, Yoseph Loyd via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi,
My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day.
Best, Yoseph _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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