[Chimera-users] Query on introducing an external protein

[Elaine Meng]

Dear Aditya,
The deleting part would be the same as described previously.

Then if you actually want to form a peptide bond between your two protein models, you can use Build Structure, the Join Models tab.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

However, that will only connect one end of the loop.  It is unlikely that the other end of the loop will be in the right place to form the bond, and Chimera will not figure that out for you.  You could try manually rotating bonds to make the other end of the new loop go to the right place, but that would probably be challenging and may give unlikely backbone conformations.   See Build Structure, the Adjust Torsions tab.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

If you got the other end of the loop in the right place, you could then add the final bind using Build Structure, the Adjust Bonds tab.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

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 Feb 5, 2014, at 6:33 PM, Aditya Padhi <adi.uoh at gmail.com> wrote:

> Dear Elaine,
>         Thank you for the detailed explanation but I think my previous query was not sufficiently clear. What I am trying to do is to insert an external protein molecule of 173 amino acids to another protein's loop region. In simple words, I want to remove 3 amino acids from one protein and there I want to place/insert another protein of 173 amino acids. So, can you suggest me whether your previous suggestion will be helpful for doing this or I have to do something else. Please let me know.
> 
> Thanking you,
> Regards
> Aditya. 
> 
> 
> On Wed, Feb 5, 2014 at 11:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Aditya,
> I'm not sure I understand the details of what you are doing, but in more simple terms, sounds like you want to (1) delete part of one protein and (2) move one protein into a certain position relative to the other protein.
> 
> For deleting, you can just select some residues and then use the menu (Actions... Atoms/Bonds... delete) or specify the residues to be deleted directly in a command, e.g.: delete #0:10-15
> (delete residues 10-15 in model #0)
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>
> 
> Just be aware that deleting is irreversible except by re-opening the original structure.  An alternative is to just undisplay that part.
> 
> There are many ways to select, including with Ctrl-drag in the Chimera window or showing Sequence (in Favorites menu) and selecting the residues from the sequence view.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
> 
> For moving one protein relative to another, that can be done by "deactivating" (freezing) one structure and moving the other, alternating with activating and moving both at the same time. It can be time-consuming.  See the "A"ctive checkboxes in the Model Panel (in Favorites menu).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
> 
> If/when you have the proteins in the desired positions relative to each other, you can save coordinates of one protein model "relative to" the other, or save coordinates of both models either transformed or relative to the same model.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>
> 
> 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 Feb 5, 2014, at 5:00 AM, Aditya Padhi wrote:
> 
> > Dear All,
> >         I want to place a protein molecule (appx. 20 kDa in size) into a viral capsid loop region which is about 7 amino acid long. What I want to do is to remove the 5 amino acids out from the loop region and place the 20 kDa protein, so that the loop region can accommodate the 20 kDa protein. I am finding it difficult as the co-ordinates of both the molecules are different.
> >
> > Although, this is not related to MD simulation or associated stuff, it would be grateful if I can get some suggestions.
> > Thanking you,
> > Regards
> > Aditya.
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 
> 
> -- 
> ********************************************
> Aditya Kumar Padhi
> Ph.D Scholar
> School of Biological Sciences (SBS)
> Indian Institute of Technology Delhi
> New Delhi-110016, India
> Contact no:+91-9711539958
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