Hi Prathvi, It would be better just to ask about ChimeraX, since that is what we are developing and recommending these days, and send your question only to chimerax-users instead of both lists. If for some reason Chimera is still needed I would mention it but those are rare cases. I will answer for ChimeraX. You can superimpose any sets of atoms that you want using the "align" command. The hard part is specifying exactly which atoms and in which order they should be paired up, but there are various command options that may be useful for this, please see the help for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 19, 2024, at 6:00 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Is it possible to superimpose/align small molecules in chimera/chimeraX?
I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences.
Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016