Question

What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both protein and RNA.

From my previous work I learned that PyMol can do alignment where it doesn't matter if the number of atoms is different, but there is problem because PyMol can only do the alignment using CA atoms, and thus it ignores my "name P" from rRNA.

I also tried to align the structures in VMD using RMSD Calculator but there needs to be same number of atoms in both selections. I also tried MDAnalysis code but there is also the problem that the selection doesn't have the same number of atoms.

Are there any suggestions on how to perform such an alignment? The best option seems to be PyMol (as it works with a different number of atoms in the two selections), but how do I incorporate the RNA into the alignment?

Answer 1

An option to align two PDB files of ribosomes with different numbers of atoms is to use PyMol or MDAnalysis. By modifying the selection commands and choosing suitable alignment algorithms, you can align both protein and RNA atoms for a successful alignment.

Step-by-step explanation:

An option to align two PDB files of ribosomes with different numbers of atoms is to use the PyMol program and incorporate both protein and rRNA in the alignment. Although PyMol typically aligns using CA atoms, you can modify the selection command in PyMol to include both 'name CA' and 'name P' to align protein and RNA atoms. By choosing a suitable alignment algorithm in PyMol, you can perform the alignment.

Another option is to use MDAnalysis, a Python library for analyzing molecular dynamics trajectories. MDAnalysis allows a flexible selection of atoms, so you can specify both protein and RNA atoms in the selection command. This enables the alignment of two structures with different numbers of atoms. By using the correct alignment method and specifying the atom names, you can achieve the desired alignment using MDAnalysis.

In summary, the best option to perform an alignment of ribosome structures with different numbers of atoms while incorporating both protein and RNA is to use PyMol or MDAnalysis. By modifying the selection commands and choosing the appropriate alignment algorithm, you can achieve a successful alignment.