Hi Ecem -
If I understand correctly, you first want to align on one set of residues
and calculate their RMSD, then to calculate the RMSD for the remaining
residues without moving the structures. This is straightforward using
PyMOL's internal command line.
```
# Create two selections called "sel1
Dear Pymol community,
I have a question about alignment module of Pymol. I have two different pdb
ids and each have about 100 amino acid long. I would like to align the
specific parts of these proteins and see both how the rest of the proteins
and also these specific parts superimpose with each ot
