Confabulating a crystal lattice for a protein model

Structure prediction has not made crystallography obsolete, but it has however made it easier — here I explore a potential trick that could be used. Under certain conditions, proteins pack in mathematically precise crystalline lattices because the lattice configuration is energetically preferable over being free in the unfriendly crystallisation solution used. Sometimes the protein will refuse to crystallise because either it is happy in solution or it would rather unfold. As a result researchers mutate surface residues to be more hydrophobic or copy the crystal packing interface ("crystal epitope") of a homologue that crystallises. A different (untested) approach could be to design the interface with ProteinMPNN or FastDesign. The catch is that one needs to make a model of the desired supercell to optimise. Here I will discuss how to make it.

A note on the Linux PyMOL C01 atom oddity

This weird bug has been haunting me for ages. The PyMOL 1.8 (not 2 in Win or Mac) and Linux PyMOL 2 builder creates residues with a Cα called C01 as opposed to CA. If any operation is done to these (e.g. Rosetta Relax), they will be discarded during the reading of the file. That is, they will not be fixed and worse if Rosetta Remodel is used, it will assume that the residue never existed, because Remodel does not understand PDB numbering annoyingly. Simply substituting all 'C01' to 'CA' fixes the problem.

PyMol on Linux without Conda

A wee note about installing PyMol on Linux for Python3 without Conda.