PCA and structural analysis help

[Former user]

Dear all,

I'm still a little new to bio3d (and R) and have been going through the worked tutorials. I'm currently studying a protein family and have generated the pdbs for each of the individual proteins using swissmodel. As much as I've tried, I couldn't quite find what I was looking for, so I will ask here...

I would like to perform a PCA based on the residue conservation (or change) across my proteins (i.e. group my sequences by AA and structural changes) and also output a pdb of the mostly highly (or least) conserved residues only (the core function doesn't really give me what I'm looking for). I'd also be very much interested in comparing subgroups of families (say 60 proteins) with a reference protein

Any help or advice you could provide me would be most welcome.

[Xinqiu Yao]

Hi,

It is not very clear what you actually want to do. Can you provide a specific example of the output or references to what you are seeking?

[Xinqiu Yao]

Closed because the user has no response.