Hi Chan Soo Khim,
The Modeller tools in Chimera (comparative modeling or adding missing loops) only model one protein chain at a time.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html>

You could “manually” put the model of the protein chain together with the RNA from the original structure:

(1) open the original structure, delete everything except the RNA (e.g. command: delete ~nucleic acid )
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion>

(2) open the protein model with loops

(3) combine those two models into a new third model (e.g. command: combine #0,1 name mycomplex model #5 )
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

However, there might be poor contacts or overlapping atoms between the protein and the RNA since the protein modeling step ignores the RNA. Typically you would model multiple different loop conformations and  look at them all together with the RNA (from the original structure) to decide which ones to keep in your model.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco