Error appears when I use customised pdb template of one domain to predict the full-length protein structure.

Hi,

I am trying to predict a protein structure which has a flexible link between two domains. I first used the AlphaFold2 MMseqs2 to generate models but the pLDDT is only 60. One domain is actually predicted very well (all blue), but the other domain is bad (red). So, I would like to use the model of the other domain to help the prediction where errors kick in.

IndexError Traceback (most recent call last)
in
47
48
---> 49 show_pdb(rank_num,show_sidechains, show_mainchains, color).show()
50 if color == "lDDT":
51 plot_plddt_legend().show()

in show_pdb(rank_num, show_sidechains, show_mainchains, color)
20 model_name = f"rank_{rank_num}"
21 view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js',)
---> 22 view.addModel(open(pdb_file[0],'r').read(),'pdb')
23
24 if color == "lDDT":

IndexError: list index out of range

Do you have any suggestions on how to fix the problem? Much appreciated!

Start at the notebook's show_pdb entry point, especially the pdb_file[0] access shown in the traceback, and reproduce the failure with a customised domain template. Inspect why no PDB file is available for the selected rank, then verify that the full-length prediction can be displayed without the IndexError.