[Chimera-users] thioester linkage between two protein

[Elaine Meng]

Dear Hamzeh,
To combine and bond the two structures, you could:

(1) open the two structures from separate input files, so that they are two different models in Chimera

(2) use the Join Models section of Build Structure (in menu under Tools... Structure Editing). This lets you specify which atoms should be removed and replaced by the new bond, the length of the new bond, etc.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

... you might need to add hydrogens before that step, since often the atoms that should be replaced by the new bond are hydrogens.  See menu Tools... Structure Editing... AddH.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>

However, this joining will not necessarily make a reasonable final model; for example, the two proteins might be intersecting one another.  After the join, you may want to rotate some bonds interactively:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

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 Jul 24, 2012, at 4:26 AM, Hamze Rahimi wrote:

> Dear Expert
> I want defiend a thioester linkage between the C-terminal carboxyl group of G and the sulfhydral group of  cysteine in the middle of other protein. Please let me know if there is such possibility in Chimera
> 
> Best wish 
> -- 
> Hamzeh Rahimi
> PhD student in Medical Biotechnology
> INT-KIT,Karlsruhe