Hi Sacha, You should be able to do this using the rms_curr command (https://pymolwiki.org/index.php/Rms_cur)
This will compute the rmsd without performing a superimposition Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 From: "CHARLTON, SACHA (UG) via PyMOL-users" <pymol-users@lists.sourceforge.net> Reply to: "CHARLTON, SACHA (UG)" <s.charlto...@warwick.ac.uk> Date: Friday, 26 February 2021 at 9:31 pm To: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net> Subject: [PyMOL] Calculating r.m.s.d values for ligands once proteins have been aligned Dear all, I hope you are keeping safe and well. I am a new user to PyMOL and had a query that I hope someone can help me with. I have performed an alignment of two homologs with the super command on PyMOL, I have generated a rmsd value for this alignment using the C-alpha atoms as comparison. Both these proteins had ligands bound, and I would like to compare how closely these respective ligands match in space/binding pose. Would someone please be able to tell me how to calculate an rmsd value now for these ligands together once the proteins have been superimposed, without changing the coordinates of the ligands? Thank you so much! All the best, Sacha
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