Dear all Thank you for looking into this.
@Keitaro: I forgot to say I am on 0.9.8.91 EL (ccp4) build. If I just refine the MDO (A/141) or residues 140-141 together, both ways, the ligand moves out of the density and the stats become all red. However, I do see that the links are there. Today I have tried the following just to test in the 7tqr PDB : -Fetch MDO residue from within COOT (success) -Delete the OXT and H2 atoms manually (success) -refine into density (success) -merge into chain A (success) Option A: rename residue (in 7tqr) to 142. The Nterminal residue is 140 and Cterminal is 144. I observe that COOT thinks there must be some sort of peptide link as it tries to link into the mainchain. Option B: keep residue inserted as 6XX. Manually "link residues" within COOT at the C and N-terminus to N-140 and C-144. -For both Option A or B - real space refinement leads to a disaster of atoms everywhere. I am still unsure the best way to move forward? ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
