Alternatively, I guess I could just cut this disordered domain into fragments, move them around and the rejoin them....
-----Original Message-----
From: Maja Divjak
Sent: Tuesday, 5 March 2024 11:44 AM
To: ChimeraX Users Help
Subject: RE: [chimerax-users] Trying to join two structures unsuccessfully
Dear Elaine,
No worries at all, I have received multiple replies, so it is working!
Thank you for your response below. Basically, it seems what I'd like to do can't really be done in this way.
In another conversation, someone mentioned the tug command. Could this yield what I'm hoping for please?
The two ends I'm trying to join are indeed in separate models, so I tried the following command:
tug #16/a:345-355 toAtoms #18/A:345-355
which gave the following error: For 0 tugged atoms expected 0 destination atoms, got 84
Would this be the correct approach (I've clearly got the syntax wrong) or is there really no way to do this in Chimera X?
Thanks so much and best wishes,
Maja
PS. How do I join the member's list please?
-----Original Message-----
From: Elaine Meng
Sent: Tuesday, 5 March 2024 11:33 AM
To: Maja Divjak
Cc: ChimeraX Users Help
Subject: Re: [chimerax-users] Trying to join two structures unsuccessfully
! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org
Dear Maja,
Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list!
So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam!
Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable.
https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds
You can see what model(s) you have by looking in the Model Panel:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html
If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first.
You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected:
info atoms sel
atom id #1/A:29@C idatm_type Cac
atom id #2/A:1@N idatm_type N3+
However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model.
https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco