How can I update a map/mesh and coordinates in a PyMol session file? 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?
Until someone identifies an ‘update’ function in PyMol, I think the next best thing is to use scripting. (See the pymol wiki) It is an imperfect solution, but it may work for the situation presented in the original post if the session may be reproduced.
To begin capturing the commands in PyMol, including menu selections to a script file, select:
File -&gt; Log File -&gt; Open -&gt; myscript.pml

When done with creating the display panels, select:
File -&gt; Log File -&gt; Close

The input data files and the script itself may then be updated or replaced. In a fresh PyMol session, execute the script with:
File -&gt; Run Script -&gt; myscript.pml

To test the above, I generated a PyMol session where I captured a script as above. I loaded the atomic coordinates of a small protein, a ligand and a 2mFobs-DFcalc electron density map. Then I displayed some panels along with mesh surface around the compound. The co-structure was then re-refined, thus generating modified atomic coordinates and electron density maps. I replaced the original files with the updates and executed the script in a fresh PyMol session. The display panels were updated accordingly.
I recommend the Advanced Scripting Workshop.