[Chimera-users] saving complex structure

[bala]

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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