This script can be used to generate a DCD trajectory file after you have loaded multiple states into a single object.
Currently, the only supported trajectory format is DCD but there will be support for other formats in the future.
save2traj (selection, name)
"name" corresponds to the output name and ".dcd" will be appended to the end of the name automatically.
The trajectory file that is generated could be numbered differently than your PDB file since PyMOL modifies the RESID values. Thus, it may be necessary to open your original PDB file and save the molecule (with modified RESIDs) to a new file. Then, load the trajectory into that new file. Alternatively, one could ..→