ValueError: min() arg is an empty sequence
Closed this issue · 1 comments
xy127 commented
Hello,
I used python version of 3.11.4 to create a conda environment and pip install igfold. I successfully finished all the example codes without issue. But when I replace with my own sequence, the following error occurs:
File "/home/ubuntu/user_space/predictantibody.py", line 10, in <module>
igfold.fold(
File "/home/ubuntu/user_space/miniconda3/envs/igfold/lib/python3.11/site-packages/igfold/IgFoldRunner.py", line 106, in fold
model_out = fold(
^^^^^
File "/home/ubuntu/user_space/miniconda3/envs/igfold/lib/python3.11/site-packages/igfold/utils/folding.py", line 221, in fold
process_prediction(
File "/home/ubuntu/user_space/miniconda3/envs/igfold/lib/python3.11/site-packages/igfold/utils/folding.py", line 139, in process_prediction
renumber_pdb(
File "/home/ubuntu/user_space/miniconda3/envs/igfold/lib/python3.11/site-packages/igfold/utils/abnumber_.py", line 63, in renumber_pdb
assert len(chain_res) == len(numbering)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError
sequences = {
"H": "EVQLVESGGGLVQPGGSLRLSCAASDFSLTTYGVHWVRQAPGKGLEWLGVIWSGGSTDYNAAFISRLTISKDNSKNTVYLQMNSLRAEDTAVYYCARDYGSTYVDAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYGSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK",
"L": "DIVLTQSPDSLAVSLGERATINCRASESVESYGNRYMTWYQQKPGQPPKLLIYRAANLQSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQSNEDPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC"
}
jeffreyruffolo commented
Hello, it looks like your sequences contain many extra residues beyond the variable domain (Fv). IgFold isn’t trained to predict this much of the structure, but if you truncate to just the variable domain it should work.