About the Align and RMSD in PyMol

Question

[Halcyon Murphy]

Hi everyone,

I am currently working on calculating the RMSD between different protein structures. 

On the one hand, I am using API in pymol (align) to get a RMSD between two models. On the other hand, I check the value of RMSD using the GUI interface Match->Align between the same models. However, I found the RMSD values are slightly different between the two methods (about 0.2 to 0.3 A). I tried to find the manual document of the align function but didn't get any detail. Does anyone know the details about how PyMol calculate the RMSD? 

e.g. are the atoms included or only backbone carbons? 
       Is the RMSD value based on every pair of atom or every pair of residues?
       What is the default parameter of the GUI align function? (I assume it's different from the API default argument)

 Thanks for your attention.

[natasha.sernova]

See this post below as an example.

Calculate Rmsd Between Two Sets Of Residues In Pymol

There are many similar ones in 'Biostars', look at the right panel.

These posts below also look helpful (they have been selected from the right panel).

Module to RMSD two proteins with Python?

Get distances between atoms with Bio.PDB

Pymol- Generating Rms Value Of Different Structures

Some Pymol tutorial may be useful too:

http://www.bch.cuhk.edu.hk/kbwong/pymol/pymol_tutorial.html

https://uzclip.net/rev/pymol+tutorial/