Last time I checked pdbset doesn't renumber the LINK, CISPEP, SSBOND records at the same time (but maybe it was fixed).
-- Ian On 26 June 2013 07:41, Francois Berenger <[email protected]> wrote: > I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly > insertion codes. > > > On 06/26/2013 03:33 PM, [email protected] wrote: > >> 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:[email protected]] *Im >> Auftrag von *MAGGIE >> *Gesendet:* Mittwoch, 26. Juni 2013 04:07 >> *An:* [email protected] >> *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 >> >>
