Re: [PyMOL] Question on rmsd alignment

[Jarrett J. <jar...@sc...>]

Hi Neena,

I wouldn't put too much stock into what you're observing in the first image
with the red arrow. PyMOL doesn't make the determination of whether that
structure is stable; but it can provide visual aid and secondary structure
assignment/hinting from coordinates and residue/atomic information.

As for the second question, Not all 177 atoms were used in the alignment to
calculate the RMSD. This depends on your alignment method and other
parameters that you set. In your case, 144 atom pairs were used for the
alignment.

Hope this helps,
Jarrett J.

On Tue, Mar 21, 2023 at 11:11 AM Neena Susan Eappen <nee...@gm...>
wrote:

> 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
>
>
>
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-- 

*Jarrett Johnson* | Senior Developer, PyMOL