I have a pdb file containing 100000 frames . Now I want to align all frame one by one in pymol and then want to save the final coordinate. How it can be done?
I would recommend using VMD. In pymol that number of frames in can be difficult to load, even if it used the command line. In VMD you could use tools as RMSD Calculator or RMSD Trajectory Tool. Save the aligned coordinates and then separate each model in an individual pdb if you want.
Unless, you mention your purpose of aligning all the frames, I would ask why would you need to align all the frames? Instead check the point where large deviations are observed and align only those frames to investigate which part is causing deviation.