Hi Tom, Thank you for your help. I can confirm that making a text file, select.py, that contains the below and running "run select.py" in the ChimeraX command line works. from chimerax.atomic import all_atoms for a in all_atoms(session): if a.scene_coord[0] < 0: a.selected = True I am quite interested in learning more about the chimerax.atomix library. Would there be any helpful resources about this? Would it be also possible to loop over a molecular dynamics trajectory and select wanted atoms in this way? Thank you. Best, Siyoung On Tue, Oct 17, 2023 at 4:06 PM Tom Goddard <goddard@sonic.net> wrote:
Oops. If you put this code in a file it needs to have a ".py" suffix, so call it select.py. The ".cxc" suffix is for ChimeraX commands.
Tom
On Oct 17, 2023, at 12:58 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Siyoung,
Here is Python code to select all atoms with x < 0.
from chimerax.atomic import all_atoms for a in all_atoms(session): if a.scene_coord[0] < 0: a.selected = True
You can type this in the ChimeraX Python shell (menu Tools / General / Shell), or probably easier, put it in a text file "select.cxc" and open that in ChimeraX to run it.
Tom
On Oct 17, 2023, at 9:04 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Siyoung, Sorry no, I can't think of a way to do it with a ChimeraX command. Maybe you could do it by using the initial orientation of the structure (just opening and not rotating) and veerrryyy carefully using the mouse to select a rectangle (Ctrl-click drag) but that is probably too difficult. Also you would need to know where X=0 is from just looking at the structure.
Certainly you could do it with Python, but somebody else would have to advise on that.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:33 AM, Siyoung Kim via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)?
Thank you. Best, Siyoung
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