Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR ....gap records for the inserted residues, cutting all peptide links. With an editor I had to change the "gap" to "TRANS" and then it worked.
Good luck! Herman ________________________________ Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von MAGGIE Gesendet: Mittwoch, 26. Juni 2013 04:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
