I noticed some strange behaviour when I do the following:
1) Load A.pdb into MacPyMOL via "pymol A.pdb"
2) Load a CHARMM simulation trajectory into object "A" via "load A.dcd, A"
3) Load a completely different structure (must have different number of atoms than A.pdb), B.pdb, into a separate/new instance/window of MacPyMOL via "pymol B.pdb"
4) Load a CHARMM simulation trajectory into object "B" via "load B.dcd, B"
Loading of this second trajectory complains with the following error:
ObjectMolecule: plugin 'dcd' cannot open file because the number of atoms in the object (4551) did not equal the number of atoms in the 'dcd' (5889) file.
In this error, the number "5889" corresponds to the number of atoms in A.pdb while "4551" corresponds to the number of atoms in B.pdb. Again, these are two separate windows of MacPyMOL (i.e. I did NOT load A.pdb and B.pdb into the same window). Somehow, the first instance of PyMOL sees what is happening in the other.
I should mention that in the real example, "A.pdb" and "B.pdb" actually have the same name but are located in different directories (in case it matters).
On a non-Mac machine, these commands are fine. As an "experienced" PyMOL user, it was quite embarrassing when a set of commands/steps that worked on a Linux workstation does not work on a Mac (especially when I was trying to show the simulations to a VMD user). I'm fairly new to Macs so maybe there's something that I need to do?
Also, when I load up B.pdb (the second structure), the MacPyMOL doesn't seem to run "hide all" and "show cartoon" from my .pymolrc.
Any help/suggestions would be greatly appreciated!