[Chimera-users] Question about peptide connection

[Marco Sette]

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,

Regards,

Marco


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
http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette


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