Works for me with PyMOL 3.1.6 and Open-Source PyMOL 3.2.0a when deleting the bonds with the "unbond" command.
fetch 4WMZ as licorice zoom elem FE unbond elem FE, * System info: Arch Linux NVIDIA GeForce GTX 1070/PCIe/SSE2 4.6.0 NVIDIA 575.64.05 PyQt5 5.15.11 (Qt 5.15.15) Cheers, Thomas On Thu, Jul 31, 2025 at 8:08 AM Takanori Nakane <tnakane.prot...@osaka-u.ac.jp> wrote: > > Hi, > > Indeed I could not show the iron as nb_spheres but I managed to use > spheres instead. > > fetch 4WMZ > as spheres, elem FE > set sphere_scale, 0.4, elem FE > > (I am using the open-source version of PyMOL 3.1.0 installed using brew) > > Best regards, > > Takanori Nakane > > On 2025/07/31 12:47, Joel Tyndall via PyMOL-users wrote: > > Hi All, > > > > I’m trying to make a pretty picture of a protein containing a heme and > > ligand. Previously I could delete the bonds (using builderthat pymol > > shows for coordination as I prefer to not show them as stick form and > > then “show nb_sphere” to show the metal ion. I can no longer do this (Fe > > doesn’t show as nb_sphere). When I select the HEM in SEQ view, it is > > still there but I cant . It is part of the HEM residue no a single ion. > > > > Using 4WMZ; PyMOL 3.1.3 > > > > Any suggestions? > > > > J > > > > University of Otago > > > > > > > > *Professor Joel Tyndall* > > > > BSc(Hons) PhD > > > > School of Pharmacy | He Rau Kawakawa > > University of Otago | Ōtākou Whakaihu Waka > > Mobile//Waea pūkoro/ +64 21 051 0940 > > > > Dunedin| Ōtepoti > > PO Box 56, Dunedin 9054 > > New Zealand | Aotearoa > > > > > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 _______________________________________________ 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
