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
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
On Mar 27, 2019, at 11:46 PM, soo khim <sookhim89@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
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@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. <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
On Mar 27, 2019, at 11:46 PM, soo khim <sookhim89@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
Hi Chan Soo Kim, You must have shown surfaces before you deleted some atoms, because the message is saying that you have surfaces for which the atoms do not exist. Close all the surface models (for example with command “surface close”) and then try to save the session. You could re-show surfaces later for the atomic structures that are in the session. Best, Elaine
On Mar 28, 2019, at 11:32 PM, soo khim <sookhim89@yahoo.com> wrote:
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@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. <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
On Mar 27, 2019, at 11:46 PM, soo khim <sookhim89@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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soo khim