Pascal
Others have covered many of the aspects you mentioned but I'll try to
answer the questions as little more directly.
On Mon, Apr 27, 2026 at 8:15 AM
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 ?
As Dale said, CDL has not affect here and there are planar restraints on the NH2 groups but non bonded clashes can force them out of plane.
It seems that may be planarity restraints associated with hydrogens are not strong enough. Is there an option to augment them ?
Yes, but it's likely something else that is the issue.
May be also the riding option only involves distance and angle restraints ?
Riding H has bond and angles but also the plane.
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
Yes. Cheers Nigel --- Nigel W. Moriarty Building 92-4-431M1, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov http://cci.lbl.gov/ ORCID : orcid.org/0000-0001-8857-9464