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, [log in to unmask] 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:[log in to unmask]] *Im
> Auftrag von *MAGGIE
> *Gesendet:* Mittwoch, 26. Juni 2013 04:07
> *An:* [log in to unmask]
> *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
>
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