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A close up of the model is shown in the right hand panel with side chains involved in clashes shown as sticks.
The analysis confirms that the change of subunit conformation is based on variation of outer environment rather than artifacts derived from the software calculation and also implies that the models we got might have a more reasonable conformation, as our model also has a better MolProbity [ 27] score than the native one which includes more steric clashes (shown in Table S1).
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com