I am afraid I always renumber - I hate insertion codes because they seem to generate so many obscure problems.. Eleanor
On Fri, 8 Nov 2019 at 19:51, Seth Harris <[email protected]> wrote: > Hi all, > > I'm sure this has been asked, but after some searching I can't find hints. > Apologies if redundant, but can someone refresh me on how to get Coot to be > graceful about residues with insertion codes...particularly during real > space refinement. I have a protease structure with very good > resolution/density but some odd numbering conventions with insertion code > (e.g. 124A, 124B, 124C between residues 124 and 125 numbering) in other > areas continuous residues have non-contiguous numbering. When doing real > space refinement both situations tend to blow apart, each individual > insertion code-numbered residue becoming its own disconnected amino acid > and well out of the density, I assume due to sterics and it not > interpreting these as being connected. Also common in Fab structures. > > I know there are painful workarounds to number it contiguously without > insertions and then add back when done refining (but then you find one more > thing...), but I am aspiring to greater elegance these days. Also hoping I > don't have to define with LINK records or such for each case? > > Thanks, > Seth > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
