Every situation has its own specific details that might make it work or not work, so I would just say to try it and see.
Even if it works, however, it might just make more sense to model the two parts separately and then use addaa to build the linker one residue at a time and then the join models part of Build Structure to join them into a single model. But which would work better depends on the details of the system and what exactly you are trying to do overall.
Also it might be much easier (unless the overall sequence is too long) to simply use ESMfold or AlphaFold to predict the overall fusion instead of Modeller.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 26, 2024, at 6:00 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
I have just one more question about homology modelling using the modeller interphase in the Chimera-X.
Would it be possible to use it for more complex tasks then the loop modeling, e.g. modeling of chimeric fusion constructs based on two given sequences and two templates in the provided pdb files ?
Many thanks in advance
Enrico