Hi,

I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in https://phenix-online.org/documentation/reference/real_space_refine.html):

hydrogens = False
main_chain = True
side_chain = True
fix_outliers = True
strict_rotamer_matching = False
auto_shutoff_for_ncs = False
secondary_structure_only = False

It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information?

Thanks,

Best,

Nicolas

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================