I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from a density map for a few figures.
Unfortunately, I wasn't quite done with refinement, and now Refmac has given me shiny new PDB and MTZ files with subtly different coordinates and terms. Is there a way to "update" my coordinates (despite the myriad groups, all the atoms still have the same name) with the new PDB? With all the groups I made that are shown/hidden/colored differently for several scenes to produce all the figures, I'd rather not recreate it all manually.
I'm more pessimistic about the map/mesh, but I created them via a script so I can repeat that. Should I also script the coordinate to figure stuff in the future if it's not finalized?