The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms. This is outside the bond length range that PyMOL accepts so the bond is absent when you display the model as line or stick model. This is why the cartoon is missing or broken. 5FUR is a 8.5 Angstrom cryo EM structure. Perhaps the associated paper explains this discrepancy.
Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: h. adam steinberg [h.adam.steinb...@gmail.com] Sent: Friday, March 20, 2020 8:57 PM To: pymol-users Subject: [EXTERNAL] [PyMOL] broken DNA cartoon Hi All, When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken and mostly missing (it should span from left to right). Any ideas on how to get the cartoon to work? Pymol version 2.3.4 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
