[Chimera-users] joining two proteins

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 8 16:00:52 PDT 2015


Hi Miguel,
It is good that you included a picture because it looks like you have selected the CA atoms.  Instead you need to select the C (carbonyl C) and the N (nitrogen) to be joined.  So, you should hide the ribbon for at least those two residues (or you could just hide all ribbon), then display all atoms of those two residues, and be careful to select only the two atoms that should get a real covalent bond between them.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 8, 2015, at 9:22 AM, López de Heredia Alonso, Miguel <mlopezheredia at idibell.cat> wrote:
> 
> Hi, 
> I am new to Chimera, so perhaps someone could give me a hand. 
> I have used Robetta for predicting the structure of a protein I am interested in and it gave back models for different parts of the protein. I would like to join them, so I am trying to join two models by a C-N peptide bond. I have selected the corresponding atoms in the last amino acid in one of the proteins and in the first amino acid of the other protein I want to join. With both atoms selected I took the “Join Models” option in “Build Structure”  with the “C-N peptide bond” selected. And the “Apply” button does not activate. (See the screen shot attached)
>  
> I have gone through the manual and I do not see what I am missing or what I am doing wrong. Any help is welcome.
>  
> Thank you very much in advance.
> Kind regards,
> Miguel




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