Hi Marco,
I'd say the "Form C-N peptide bond" function in the Join Models section of the Build Structure tool would be better suited to this.  The chains being joined have to be in different models, so to accomplish that you open your model twice and in one of the models you would delete the chain that includes :41 and in the other you would delete everything except the chain that includes :41.
If you are using Chimera 1.20, you either have to use tomorrow's daily build or a previous version of Chimera, because the 1.20 version of Build Structure has a bug in it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Sep 3, 2026, at 3:10 AM, Marco Sette via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi all,

I'm following the procedure reported in a previous message to connect the ends of a peptide.

In my case

~ribbon
display
delete :41@oxt
bond :1@n: 41@c

After, I run minimization, but I have the following message

Charge model: AMBER ff14SB
Total charge for #0: 0.810
The following residues had non-integral charges:
    SER 1.A 0.8102
1 model(s) had non-integral total charge
Details in reply log
Residue #0:1.A (SER/serine)  is missing atom H_1

In my model SER1 has two hydrogens named H2 and H3. Now the nitrogen has four covalent bonds that is unusual.

If, before connecting residues 1 and 41, I add hydrogens to the molecule I obtain SER1 with 3 hydrogens. After I remove H2 and H3 and repeat the procedure, in the minimization step I obtain the message that H3 is missing...

Any suggestion?

Thanks

Marco



-- 
Marco Sette, PhD
Associate Professor of Molecular Biology 
Department of Chemical Sciences and Technology 
The University of Rome, "Tor Vergata"
Via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette@uniroma2.it
Tel.: +39-0672594424
Fax: +39-0672594328
_______________________________________________
Chimera-users mailing list -- chimera-users@cgl.ucsf.edu
To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu
Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/