[Chimera-users] building on functional groups

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 21 11:06:15 PDT 2014

Hi Jesse,
You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools… Structure Editing).  It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works.  Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type.  You would add hydrogens (could do with AddH the first time around… this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type.

See the following (or click Help on the tool dialog)

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

On Oct 21, 2014, at 10:55 AM, JESSE JAYNES <jjsqrd at bellsouth.net> wrote:

> Folks:
> I was wondering if I could get help with something.  I have a peptide with a peptide with lysines and I would like to add acetyl groups to them.  Is that possible?  Thanks, Jesse

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