[Chimera-users] Question about peptide connection

Marco Sette sette at uniroma2.it
Mon Jul 26 14:58:48 PDT 2021

Hi Nicole,

you could  note the pdb name of the old structure and use the homology 
modelling tool provided in Chimera (it is based on Modeller then you 
need a password to access the server) to model the new sequence, using 
the old one as a template. Check that the alignment is correct 
(identical alignment except the new region) and let the server prepare 
your structure.

Hope it helps,



Il 26/07/2021 21:19, Nicole Ostrovsky via Chimera-users ha scritto:
> Hello,
> I have a structure which I've cut a section out of and I am working on 
> connecting the two loose ends together. I wanted to connect them with 
> two glycine residues - since they are easiest to work with and have no 
> side chains. I am doing this using the Modify Structure option under 
> the Build structure tool and adding one atom at a time. However, when 
> I try to minimize my newly created glycine, I get the error message 
> "No MMTK name for atom "H1" in standard residue "GLY"" (I've attached 
> a picture of my reply log). I'm not sure how to troubleshoot this.
> Is there a better way to connect two ends of a peptide, or should I 
> change the way I am using the modify structure tool?
> Thank you.
> Nicole Ostrovsky
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Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail: sette at uniroma2.it
e-mail: m77it at yahoo.it
Tel.: +39-0672594424
Fax: +39-0672594328

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