Building An Average Consensus Structure

Question

[Harpalss]

I have a 4 pdbs which have at least 85% sequence similarity from the query sequence. What would be the easiest way to build an average structure from the four pdbs?

Answer 1

[João Rodrigues]

I don't know how valuable that information might be. If you try to average atomic coordinates you'll end up having, most likely, clashes and bumps, not to mention overall artificial stereochemistry. You're probably better off building a homology model based on 4 templates using MODELLER for example. There is an example in their tutorial where they use 4 templates to build a model - Advanced Modelling.