[Chimera-users] Query on introducing an external protein

Aditya Padhi adi.uoh at gmail.com
Wed Feb 5 18:33:06 PST 2014

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,

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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