Re: [PyMOL] Difference between backbone and heavy atom RMSD and how to calculate them in PYMOL

Hi Santrupti, In Chemoinformatics "heavy atoms" are all non-hydrogen atoms. In crystallography, "heavy atoms" could mean the atoms used for experimental phasing, like selenium. I hope these examples answer your questions: # non-hydrogen RMSD align prot1 & not hydro, prot2 & not hydro,

[PyMOL] Difference between backbone and heavy atom RMSD and how to calculate them in PYMOL

Hi, I want to calculate pairwise RMSD for heavy atoms and backbone atoms. I see that for backbone, I can use name n+c+ca+o. But, do the same atoms also represent heavy atoms? What are the differences between backbone and heavy atoms? How to compute pairwise RMSD for a lot of structures? Can I