[Chimera-users] saving complex structure

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 2 09:52:39 PST 2008

Hi Bala,
In the future it would help us to answer your questions more  
specifically if you would say which structure you are using (if it is  
available from the PDB).

First you would display ONLY the RNA, then save displayed atoms.   
Then display ONLY the protein, save displayed atoms.  Close the  
original file, open the two new files.  One should have only the RNA,  
the other should have only the protein.  Example (with commands but  
you could also use menus/GUIs):

open 1vbx
show protein
write displayed relative 0 0 /Users/meng/Desktop/myprot.pdb
show nucleic acid
write displayed relative 0 0 /Users/meng/Desktop/myrna.pdb

Or, a different way to make the two files would be to delete  
everything EXCEPT the RNA, then save PDB, then open the original file  
again, delete everything EXCEPT the protein, then save again.

With manual docking you will want to "freeze" one structure and move  
the other.  You can freeze/unfreeze individual structures ("models")  
by unchecking/checking the "Active" boxes in the Model Panel (under  
Favorites) or the small boxes shown under the Command Line.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 1, 2008, at 9:57 PM, bala wrote:
> Dear chimera friends,
> I have a protein-RNA complex pdb structure. I want to remove the  
> RNA in the crystal structure and put my RNA molecule in to the  
> binding site.
> Since my RNA is very big around 20bp long, i prefer to manually  
> dock my RNA followed by a big simulation than a automated docking.  
> I tried in chimera and i saved the complex structure with the  
> option "save the displayed atoms". But when i see the pdb  
> structure, it has the coordinates of RNA molecule but not the  
> protein.  Also when i open the pdb in chimera, it shows me the  
> protein structure.  Kindly write me your comments on using chimera  
> i) for such a manual docking and also ii) how to save the complex  
> structure.
> Wish you all a happy new year,
> Bala

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