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@case.edu> wrote:

 Dear chimerax-users@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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