Problem with showing 4 Fe-4S in pdb with chimerax
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
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 <mailto: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>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks a lot! I've tried both methods, they work very well. On Wed, Apr 22, 2020 at 12:37 PM Eric Pettersen <pett@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@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> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Eric Pettersen -
Meinan Lyu