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. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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