Hi All, 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.
Has anyone experienced this issue before? Maybe I am missing something. Thanks a lot in advance, Hauke ------------------------------------------------------- Hauke Hillen Department of Molecular Biology Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11 D-37077 Göttingen Germany E-Mail: [email protected]<mailto:[email protected]> Phone: +49-551-201-2864 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
