[chimerax-users] Re: Aligning two ligands

Hi Elaine, awesome, thanks. I was so fixed on trying to make it work with the "match" command that I didn't think a bit further. I'll give it a go asap. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:33acbe4d-b70c-4f4c-b57b-1d05096f21f9] ________________________________ From: Elaine Meng Sent: Friday, June 23, 2023 5:50 PM To: Karim Rafie Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Aligning two ligands 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Falign.html&data=05%7C01%7Ckarim.rafie%40umu.se%7C053aab51ada6444f52fe08db74019477%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638231322422863693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=cZirz9JJLyHg8tdnngZusfS4M331jb9lyH%2FeBAHINLY%3D&reserved=0https://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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Findex.html%23commands&data=05%7C01%7Ckarim.rafie%40umu.se%7C053aab51ada6444f52fe08db74019477%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638231322422863693%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RWGgzL0xJ9O7UX95cjTDIZiQIJxWkRVhwc6GnSiNrZE%3D&reserved=0https://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 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