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
