[Chimera-users] chimera utility help

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 17 09:38:51 PDT 2012

Dear Sotirios,
You would use Join Models option "C-N peptide bond" as described in these instructions:

"C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond."

If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version.  If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport.

I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote:

> Dear Elaine C. Meng,
> I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25 at C) and the N terminus of the protein (#1:26 at N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you.
> Best Regards,
> Sotirios Katsamakas.

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