Hi Pascal, perhaps this is relevant re NH2: https://journals.iucr.org/d/issues/2020/12/00/qj5005/qj5005.pdf For the ribose check GeoStd cif file to see exactly what restraints are applied for a particular H: mmtbx.where_is_that_cif_file CODE Pavel On 4/27/26 08:14, [email protected] wrote:
Dear all,
I am trying to refine a high-resolution cryo-EM structure. However, some of the guanine NH2 groups end up out of plane (I used cdl). Is that an expected behavior ?
It seems that may be planarity restraints associated with hydrogens are not strong enough. Is there an option to augment them ? May be also the riding option only involves distance and angle restraints ? This is not clear from the manual to me.
Also, for OH groups like ribose 2'-OH groups, I assume that the riding option only involves distance restraints and that these H-atoms are otherwise free to rotate
Can you please help me out here ?
Thanks, Pascal _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s