Re: [PyMOL] Fe in heme disappears

[Thomas H. <th...@th...>]

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
<tna...@os...> 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
> >
> >
> >
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