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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>
>
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