[Chimera-users] adding GalNac moiety on Threonine residue

[Elaine Meng]

Hi Elsa,
(A) One way would be to open some additional PDB entry that has a GalNac in it, deleting all the other atoms in that structure except for one GalNac, and then using the Join Models section of Build Structure (in menu under Tools… Structure Editing) to stick the GalNac onto the threonine in your protein complex structure.  You may need to add hydrogens first. Join Models also requires you to enter the desired attachment bond length and angles, which you could determine by measuring them in some example glycosylated structure.  You could open yet another glycosylated structure in the same Chimera and temporarily hide the other stuff while you do the measurements, then close that example structure and unhide the others, or just start another instance of Chimera to open and measure the example structure.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#structuremeas>

(B) Another way would be to again open an additional PDB entry that has a GalNac glycosylation, deleting all but the GalNac and the attached residue, superimposing that on the threonine in your structure, deleting the attached residue, and then merging the two structures.  The tricky part might be superimposing the structures adequately, and approaches for that could include the "match" command and specifying exactly which atoms to fit and/or manual positioning.  These methods are mentioned in the superposition page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
Merging can be done with "copy/combine" in the Model Panel (under Favorites in the menu) or the command "combine":
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
Then you would still need to add the bond with the "bond" command or the Adjust Bonds section of Build Structure (in menu under Tools… Structure Editing).

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

On Jan 28, 2014, at 10:07 AM, Elsa Marquez <emarquez at ualberta.ca> wrote:

> Hi there! 
> Do you guys know if I can add or somehow draw a carbohydrate moiety such as GalNac to a single Threonine in a protein complex? 
> Thanks! 
> Elsa Marquez 
> University of Alberta