Missing Residue Modeling for an Oligomer Inquiry
Hello, I missing residue modeled a loop region of a monomer from an oligomer heptamer and then oligomerized this new model monomer via GalaxyWeb into a heptamer, however, the generated heptamer´s RMSD to the PDB structure is a great 40 A.
My understanding is that my above methodology is how Modeller would function best due to interfacing of multiple subunit problems if I tried to missing residue model all seven loops with missing residues. Is it possible to try and missing residue model the complete heptamer regardless due to my generated heptame exhibiting an unsatisfactory RMSD Value?
Thanks
On 9/19/22 9:29 AM, Joel Subach via modeller_usage wrote: > Is it possible to try and missing residue model the complete heptamer > regardless due to my generated heptame exhibiting an unsatisfactory > RMSD Value?
Yes, I would try to model all 7 chains simultaneously in Modeller. Since the rest of the protein will be held fixed during the procedure, the final structure should have a low RMSD to the original PDB.
Ben Webb, Modeller Caretaker
Hi Ben thank you so much for your kind update:)
On Mon, Sep 19, 2022 at 7:28 PM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 9/19/22 9:29 AM, Joel Subach via modeller_usage wrote: > > Is it possible to try and missing residue model the complete heptamer > > regardless due to my generated heptame exhibiting an unsatisfactory > > RMSD Value? > > Yes, I would try to model all 7 chains simultaneously in Modeller. Since > the rest of the protein will be held fixed during the procedure, the > final structure should have a low RMSD to the original PDB. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Joel Subach -
Modeller Caretaker