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

 

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Friday, June 23, 2023 5:50 PM
To: Karim Rafie <karim.rafie@umu.se>
Cc: chimerax-users@cgl.ucsf.edu <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=0>

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=0>

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>