On 08/04/2019 18:40, Hillen, Hauke wrote: > > > Lately I have been having a strange issue with Coot (0.8.9.2-pre on > MacOS X). Sometimes when I add residues using “Add residue…”, they are > not linked to the previous residue. When I try to real space refine / > normalize they behave as if they were part of the chain, but the atoms > that should be covalently bound to each other (peptide bond for > protein or P and O3 for nucleic acids) appear to be repelled. So Coot > apparently treats them as separate chains during refinement also. The > residues are obviously in the same molecule and chain and have > consecutive numbering. Oddly, this appears to happen to particular > residues (for example always residue 4 in a chain, not 3 and not 5, > even if I delete them all and start adding again with “Add residue”). > It appears to happen most frequently when I delete residues and re-add > them. I checked the PDB file whether there is anything suspicious > about the respective atom records for the misbehaving residues, but > they appear fine. >
That sounds weird and doesn't ring any bells sadly. I'd just recommend that you make sure that you are not doing post-refinement: set_add_terminal_residue_do_post_refine(0) But maybe that is already the case in the version of Coot that you have. You can usually anneal broken peptide bonds with triple-refine (bound, by default, to the "T" key). Regards, Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
