How to Treat Two Chains as a Single Entity

[hanjialu0810]

Hello,

I am working with two PDB files, each containing three chains: E, F, and B. I need to analyze the interface interactions between chains EF (considered as a single entity) and B. Could you suggest a method or tool that allows me to treat EF as one unit for this analysis?

Additionally, I have a question about the -allowed_mismatches parameter. Does this parameter mean that the specified number of mismatches in the sequence alignment will be ignored during the analysis? If so, do these mismatches affect the interface interaction analysis when they occur within the interface regions?

I appreciate any help or suggestions you can provide.

Thank you!

[clami66]

Hi,

See issue #33 for information on grouping chains.

about the -allowed_mismatches parameter. Does this parameter mean that the specified number of mismatches in the sequence alignment will be ignored during the analysis?

All residues, including mismatching ones, are included in the analysis. Increasing the number of allowed mismatches only influences how the tool groups together template-target chains, but the rest of the analysis is performed in the same way