[PyMOL] Question on rmsd alignment

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

1. I see this unusual secondary structural element in the peptide structure
shown below. It was generated from computations, so the unusual element
arose from positive dihedral across lysine residue. My question is whether
it is structurally possible or if it is a stable structure?
[image: image.png]
[image: image.png]

2. Also when using alignment tool on PyMOL for the below two structures,
RMSD is displayed with a certain number of atoms in parentheses (144
atoms). However, there are 177 atoms in total. So does this RMSD mean that
the total difference in RMSD between these two structures is 0.602
Angstroms and only 144 out of 177 atoms with very close alignment/
position?

RMSD =    0.602 (144 atoms)
[image: image.png]
Any insight would be appreciated!

Thank you so much for your help,
Neena