[PyMOL] Morphing question

[Istvan K. <iko...@gm...>]

Hi,

I have a homo trimer protein structure in two different conformations.
However, one conformation has different atom ordering and an additional
residue. This has never been a problem, though, since align does sequence
alignment, so I am not sure why morphing (Pymol 2.5) gives completely crazy
morphing frames with atoms all over the place. The only difference is that
this is a homo trimer as opposed to a single chain protein. Could a homo
trimer somehow confuse the morphing algorithm?

As an example, I attached 3 PDB files. A.pdb can be morphed to B.pdb
perfectly fine, but morphing A2.pdb (which is very similar to A.pdb) to
B.pdb gives the crazy results I mentioned.

Thank you for your kind assistance.

Best regards,

   Istvan