Hi Karim, The command for aligning any sets of atoms is "align" (whereas "match" = "matchmaker" and is for biopolymers only since it uses sequences). Use command "help align" to see the manual page, or view the copy at our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> The matchmaker and align pages already crossreference each other, but I will try to make it more obvious. You can also scan the list of commands in the User Guide to try to find a particular function: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2023, at 6:44 AM, Karim Rafie via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
I was wondering if there's a command that will allow me align two ligands to each other? Couldn't find anything online and when I try the match command I constantly run into an error, even when specifying certain atoms between two ligands.
Any help would be greatly appreciated.
All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden <Outlook-i50n4zlk.png>