Hi Kevin, This is the kind of research decision that you will need to make yourself, considering that (as far as I know) there is no generally accepted obvious right answer and that nobody is as invested in your own research project as you are. It could be that one type of comparison is better for highlighting certain characteristics, whereas the other is better for highlighting others. You might even want to include both in your discussion. As for superposition of the atomic structures, you can do it in ChimeraX with matchmaker (which tries to figure out residue equivalences for you, uses CA atoms only for fitting, and by default, iterates so that the common core superimposes more tightly at the expense of the more different areas) or align (where you have to specify exactly which atoms to use for fitting and also has an iteration option). You will also get slightly different results if you use different parameters/options with each of those approaches, e.g. whether or not fit iteration is done. Slight differences may not even be significant to your conclusions, considering the error bars of atomic coordinates, protein flexibility, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 9, 2023, at 2:31 PM, Kevin Felt via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimerax Developers,
There is a debate in my lab about the best way to compare two PDBs of the same protein bound to different ligands; the goal is to identify subtle differences in the binding pocket between the ligand-bound conditions. One method of comparison is to fit the two density maps together using the FitMap function, and then fit each PDB into their respective maps which have been aligned. Another way is to simply align the two PDBs (such as the align function in Pymol). Using these two methods results in slightly different alignments of the PDBs and thus give slightly different positional differences of the binding pocket and ligands. The resolution of these density maps range from 2.4 - 3.5 angstroms. Which way would be the more accurate way to look at the differences between two similar models? Thank you!
Sincerely,
-- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University