Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html> To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window. The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log. I hope this helps, 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 Aug 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico