[Chimera-users] Adding sugars to protein at specific amino acid glycosylation site

[Elaine Meng]

Hi Tommy,
I'll answer the second part first since it is simpler.  You can just open more than one structure file in the same Chimera.  There is no need to do any merging.  Each structure file you open becomes a "model" in Chimera.  You can move one relative to the other by freezing/unfreezing them individually and using the mouse to move only the unfrozen ones.  This is called "activating/deactivating" a model for motion, and there are several ways to do it:

   - checking/unchecking the A(ctive) boxes for the model in the Model Panel (show Model Panel using Favorites menu)
   - checking/unchecking the boxes under the Command Line (show Command Line using Favorites menu)
   - etc. as detailed here  <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

Independent of activation status, you can also move models together or separately with various commands (move, turn, etc.) but I am guessing you wanted to move them interactively with the mouse.

OK, now the first part of your question.  Yes, there are tools available for manually building structures in Chimera, even atom-by-atom, or if you have the two parts (e.g. a protein and a carbohydrate chain) already open as separate models, you can join them into one model with a bond.  See the Build Structure tool, tabs: Start Structure, Modify Structure, Join Models.  This tool is in the menu under Tools… Structure Editing.   One possible way to get the carbohydrate chain as a model in Chimera is to open a structure that has the glycosylation that you want, then delete all the other atoms except for that glycosylation group.  See also this previous reply to the mailing list:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009568.html>

However, for adding glycosylations it might be easiest for you to use this GlyProt web server:
<http://www.glycosciences.de/modeling/glyprot/php/main.php>

I haven't tried it myself, however.

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 Nov 24, 2014, at 8:50 PM, T T <jollygood11967 at gmail.com> wrote:

> Dear Mr/Ms,
>  Good morning. My name is Tommy from San Diego Biomedical Research Institute. I am currently learning to use the chimera software. Great work in creating a program for protein and DNA visualization.
> 
> I have one question to ask regarding the subject above. Is there a way to manually add sugar component onto an existing pdb file?
> 
> To be precise, I am currently working with HIV-1 envelope. I have the pdb files that features the structure of HIV-1 trimer Env. I wanted to add glycan at specific sites to show steric hindrance to antibody binding.
> 
> Another question.
> Is there a way to superimpose 2 pdb files into one image? For example, I have one pdb file for HIV-1 Env and another pdb file for antibody. Can I "merge" these two pdb files as one image?
> 
> Also, assuming that it is possible to "merge" two different pdb into one image, is there a way to rotate one protein without affect the orientation of the other protein?
> 
> Any advice/tip is greatly appreciated.
> Thank you.
> 
> Sincerely,
> Tommy