Select all connected atoms to selection
Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command select @{atom_name}; select zone select 2 It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks!
Alex, My SEQCROW plugin adds a selector for everything on the same fragment as the current selection. It only looks across bonds, not pseudobonds (e.g. metal coordination or H-bonds). The selector is `connected`, so you'd run `select @{atom_name}; select connected`. If you want to do this interactively, it also adds a mouse mode that lets you click on a fragment to select it. You would need to restart ChimeraX after installing for the mouse mode menu options to show up. Plugins can be installed via Tools -> More Tools... on the ChimeraX menu. Best, Tony On Tue, Sep 10, 2024 at 1:43 PM Alexander Lee via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command
select @{atom_name}; select zone select 2
It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks! _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Alex, Tony's suggestion is excellent if you are trying to selected the entire connected fragment, but from the command you're currently using it seems like you are only trying to select the atoms directly bonded to the currently selected atom. If so, then this Python code will do that: from chimerax.atomic import selected_atoms selected_atoms(session).neighbors.selecteds = True If you put the above into a file whose name ends in .py (e.g. "sel-bonded.py"), then you can use ChimeraX's open command to open that file, which then runs the code. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Sep 10, 2024, at 12:41 PM, Alexander Lee via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command
select @{atom_name}; select zone select 2
It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks! _______________________________________________ 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/
participants (3)
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Alexander Lee -
Eric Pettersen -
Tony Schaefer