[Chimera-users] Query on introducing an external protein

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 5 09:32:21 PST 2014


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.
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> Chimera-users at cgl.ucsf.edu
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