Re: [PyMOL] Pymol-Alignment Module

[Jared S. <jar...@co...>]

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" and "sel2"
select sel1, resi 1-20
select sel2, resi 30-100

# Note: if the numbering is different between the structures, you may need
something like this instead:
# select sel1, (struc1 and resi 1-20) or (struc2 and resi 2-21)

# Superimpose the structures (this prints the RMSD to the console)
super struc1 and sel1, struc2 and sel1

# Calculate the "in-place" RMSD for the remaining residues (also printed to
the console)
rms_cur struc1 and sel2, struc2 and sel2
```

Note that if there are any residues with alternate conformations, or if the
numbering is different between the two structures, the `rms_cur` step may
need to be modified as indicated in the examples on its wiki page
<https://pymolwiki.org/index.php/Rms_cur#Examples>.

Hope that helps.

Cheers,
Jared


On Fri, Mar 4, 2022 at 5:37 AM Ecem Güngör <ece...@gm...> wrote:

> 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 other. In other words,
> if I align the proteins based on their 20-30 amino acids, I would like to
> first see what the RMSD is for these specific regions (20-30 aa) and then
> the RMSD of the rest (1-20 and 30-100) is. I truly appreciate your
> suggestions and guidance on this. Thank you!
>
> Have a great week/weekend,
> Ecem
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