Words - use WORDS - what does "the T key" mean in plain English!!!!!!!
Eleanor On Mon, 8 Apr 2019 at 18:59, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
