[PyMOL] Align command and alternate residue conformations

[João C. M. R. <ra...@mb...>]

Dear all,

I would like to compare two crystal structures of the same protein, one obtained by X-ray diffraction and the other by neutron diffraction. I used the Align command in PyMOL with zero cycles of refinement to align these structures and obtain a rmsd between all non-H/D protein atoms. However, I would like to understand how Align calculates the rmsd, specifically how does it handle alternate residue conformations. Does it pair side-chain conformations based on their name (e.g. A, B, C..) or on their spatial proximity (i.e., conformations are paired regarding their position). I can imagine 2 scenarios that might be problematic: 1) where the side-chain conformations closer in space have different names; 2) where one structure has a double side-chain conformation, and the other has a single conformation.

Best regards,
Joao Ramos