Yingyao Zhou

Yes, the results are correct. Thanks!

I wonder if this insertion code checking is really necessary. If I comment it out, ColabFold seems to work. It would be great to get your expert's opinion. Thanks. in...

[1crn.pdb.txt](https://github.com/sokrypton/ColabDesign/files/11479548/1crn.pdb.txt) Using the following toy example, the output from fix_partial_contigs becomes A1-44, and this then leads to incorrect output for fix_pdb, (chain E should have been renamed to B, but...

I tried this barebone version, still got the exception that I cannot catch and cannot suppress. I have also reinstalled dask: pip3 install "dask[complete]" --upgrade --force-reinstall Really appreciate your insights....

I use cif-seqres, because we need to extract the residues that are missing in the coordinate portion of cif. Cif-atom will miss those. But we would like the chain name...

Thank you for the quick response. Here is a test code ``` seq1="IELTQSPSSLSASLGGKVTITCKASQDIKKYIGWYQHKPGKQPRLLIHYTSTLLPGIPSRFRGSGSGRDYSFSISNLEPEDIATYYCLQYYNLXRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYSKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE" seq2="IELTQSPSSLSASLGGKVTITCKASQDIKKYIGWYQHKPGKQPRLLIHXTSTLLPGIPSRFRGSGSGRDYSFSISNLEPEDIATYYCLQYYNLXRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYSKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKXXXERHNSYTCEATHKTSTSPIVKSFNRNE" from Bio import pairwise2 from Bio.pairwise2 import format_alignment match, xmatch, gap_open, gap_ext = 2,0,-1,-0.2 alignments =...

Thank you all for your willingness to help! I believe Peter’s suggestion could be a good solution. My main goal is to optimize terminal space usage so that sequences can...

Thank you. However, it's not clear to me how to use this. How do I set the terminal_columns? Not sure how to test. On Wed, Sep 17, 2025 at 5:34 ...

I don't know what's wrong. I ran "pytest Tests/test_Align_Alignment_format.py" and it was clean.

I believe I have fixed the style issue in the test script. The error currently is in the main code. https://ci.appveyor.com/project/biopython/biopython/builds/52789718 I don't feel comfortable to add this new attribute...