Thank you, guys. My problem has been solved. AutoMR in CCP4 removed the insertion code. But I used it before, and it did not mess up with the insertion code at those times.
Rain On Thu, Jun 27, 2013 at 12:56 PM, Ian Tickle <ianj...@gmail.com> wrote: > 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 <beren...@riken.jp> 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, herman.schreu...@sanofi.com 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: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 >>> >>> >
