One of the key bindings in Coot. Need to center on a residue surrounded by a residue on the left and the right. Press "Shift+T" and Coot will refine the three consecutive residues. There might be the refinement quality window popping up, though I'm not sure. There is another keybinding "h" or "shift H" which does basically the same but "auto accept" the refined state......or actually the other way around.
On Mon, Apr 8, 2019 at 9:37 PM Eleanor Dodson < [email protected]> wrote: > Words - use WORDS - what does "the T key" mean in plain English!!!!!!! > > Eleanor > > On Mon, 8 Apr 2019 at 18:59, Paul Emsley <[email protected]> > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
