How to reduce clashes efficiently when building a cryoEM structure? Real space refinement always results a clash score bigger than twenty. Manual optimization in Coot doesnt work well.
I also ran into this issue, how did you solve it later?
Hi wangl,
I subsequently found it was caused by the un-calibrated physical pixel size of cryoEM and it was solved after re-calibrateing pixel size.
Best,
Lai
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Do you know how to calibrate pixel size, when validation in PDB website?