[Chimera-users] rna-protein complex

soo khim sookhim89 at yahoo.com
Thu Mar 28 23:32:02 PDT 2019

Hi Elaine,
Thanks for the useful tips. 
I encountered another problem when I tried to save the session.The pop out shows : cannot save surfaces without associated structure. Surface will not be saved".
What can i do to resolve this? I have surfaces in the model.
Thank you
Best Regards,
Chan Soo Khim


    On Friday, March 29, 2019, 12:16:43 AM GMT+8, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 Hi Chan Soo Khim,
The Modeller tools in Chimera (comparative modeling or adding missing loops) only model one protein chain at a time.

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 )

(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 )

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 C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 27, 2019, at 11:46 PM, soo khim <sookhim89 at yahoo.com> wrote:
> Hi chimera,
> I have a RNA-protein complex pdb file. After modeled the missing loops in the protein and saved the pdb file for remodel protein structure, the RNA is missing in the new pdb file. How should i save the remodel protein model together with its RNA?
> Thank you
> Best Regards,
> Chan Soo Khim
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