[Chimera-users] ligating two models

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 6 09:35:46 PDT 2013

Hi Bala,
Usually the best way is with "join models" (menu: Tools… Structure Editing… Build Structure, go to "Join Models" section).  You specify bond length and torsion angle for the join, and it will move one model accordingly.   You also have to select one atom on each model to replace, so you may need to add hydrogens first, depending on the chemistry of the join.  For example, to phosphorylate a serine you would replace the OH hydrogen of the serine and one of the phosphate oxygens with the new bond.  You can change the bond length and torsion later if you need to, using the "Adjust Bonds" and "Adjust Torsions" sections of Build Structure.


The other way is longer and more difficult, unless you have already (A) moved the models into exactly the right relative position to form the bond.  The following steps would be to (B) combine the models into one new model with "copy/combine" in the Model Panel or the "combine" command and (C ) add the bond with the "Adjust Bonds" section of Build Structure or the "bond" command.  You have to combine first because Chimera does not allow bonds between different models.

I hope this helps,
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 6, 2013, at 3:32 AM, Bala subramanian <bala.biophysics at gmail.com> wrote:

> Friends,
> What is the best method in chimera to ligate two models. I have generated a small ligand that has to be attached attached to a protein residue.  
> Thanks in advance,
> Bala
> -- 
> C. Balasubramanian

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