Hello,
I am using Chimera (Modeller) to model a loop, which locates at the C-termini of the original crystal structure. The structure of the target protein is a homodimer, however, I cannot model the two chains together. How can I model the two chains together? I modeled chain A and chain B separately, the loops I modeled have different configurations.
Could you please help me resolve the problem?
Best regards, Rui
Hello,
I have a follow-up question, I modeled only one of the two chains, after I modeled the loop to the chain, I saved it as a pdb file using Chimera. I realized the saved pdb file changed the beta factors to almost zero and changed the atom orders within each residue. How can I model the loop without affecting the original structure?
Best regards, Rui
On 8/15/19 8:27 PM, Rui Chen wrote: > I realized the saved pdb file changed the beta factors to almost zero > and changed the atom orders within each residue. How can I model the > loop without affecting the original structure?
This is not possible without some major alterations to your copy of Modeller.
Ben Webb, Modeller Caretaker
On 8/15/19 6:44 PM, Rui Chen wrote: > I am using Chimera (Modeller) to model a loop, which locates at the > C-termini of the original crystal structure. The structure of the target > protein is a homodimer, however, I cannot model the two chains together. > How can I model the two chains together?
I don't know if you can do it in Chimera - you would have to ask the Chimera folks. It is definitely possible in Modeller directly though - just specify both loop segments in your loop modeling script. See https://salilab.org/modeller/9.22/manual/node36.html in particular the commented-out "Too loops simultaneously" part of the script.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Rui Chen