[chimerax-users] Problem with showing 4 Fe-4S in pdb with chimerax

[Meinan Lyu]

Thanks a lot! I've tried both methods, they work very well.

On Wed, Apr 22, 2020 at 12:37 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Meinan,
> The problem is that your file lacks CONECT records.  In the absence of
> CONECT records it adds incorrect (in this case) distance-based bonds.  If
> you look at the normal 2WDQ entry, which does have CONECT records, the F3S
> moiety is correct.
> So you need to add CONECT records.  You could do it by hand, which would
> be tedious.  Perhaps PyMOL can write out a PDB file with CONECT records?
> You can also delete just the Fe-Fe pseudobonds with this command:
>
> sel Fe ; del pb sel
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On Apr 21, 2020, at 7:17 PM, Meinan Lyu <mxl1032 at case.edu> wrote:
>
>  Dear chimerax-users at cgl.ucsf.edu，
>
> There is a 4 Fe-S in my structure, it shows a little bit funny when I open
> it with chimerax. It should only have links between Fe and S, but
> between 2Fe shows a link line two. Do you know how to show it normally like
> in pymol, or remove the links between 2Fe? I really want to draw some
> figures in chimerax. The attached are  4 Fe-S shown in chimrax,also shown
> in pymol. PDB id 2WDQ is also attached, which  4 Fe-S is in /B,F,J:303.
> Thanks very much.
>
> Be safe and Best,
> Meinan
> Postdoc from CWRU
> <fe-s_chimerax.tif><Fe-S_pymol.png><2WDQ.pdb>
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