Hi Dmitry, I’ve come across this once or twice… I would say the more likely cause is that the monomer was created/refined in absence of its symmetric copies, rather than the symmetrization itself, so there was no information to guide it at the interfaces. My process has been to place just the neighbour copies around one monomer, refine that all-together, adjusting the interfaces as much as possible to reduce clashes (on the monomer only), then using that fixed central monomer to produce the symmetric complex. This should reduce clashes and is somewhat simpler than refining/adjusting all 14 at the same time for example. hth Greg
On Jun 7, 2023, at 4:41 AM, Dmitry A. Semchonok via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear colleagues, I want to symmetrise the monomer to get the complete model that has D7 symmetry. I symmetrised the monomer getting the complete 14-homoligomeric model.
The issue is that the PDB validation report shows the presence of many clashes.
Do I understand correctly that if the symmetrisation goes correctly, the clashes are not present? Did the symmetrisation go wrong due to the incorrectly measured symmetry centre? What are the options to fix that?
Thank you for your opinion.
Kind regards, Dmitry
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