[Chimera-users] Question about peptide connection

[Elaine Meng]

Thanks, Marco -- good idea!  It might give a more reasonable result than manual building + minimization.

Nicole, see:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>

Elaine

> On Jul 26, 2021, at 2:58 PM, Marco Sette via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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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