Running PCA/eNMA on homological structures

[Former user]

Hello Bio3D community. I am currently working with a ligand binding protein, and have aligned it with around 400 structures. However, there are some proteins that are much larger than the protein we're trying to align them to (our protein is about only 1 chain of proteins). Furthermore, I was wondering if we need to cut the chains to only where our protein is aligning to. Or, is it okay for us to keep the whole protein and only focus on the part that is aligning. Thank you so much!

[Xinqiu Yao]

It is okay to keep the whole chain and just analyze the part your protein aligned to. Just make sure the alignment is correct by using, e.g. Seaview, to visually check.

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