Hi Luca,
You should not settle for poor results here. With the most recent CCP4 and
PDB-REDO versions refining with an N-terminal CXM works fine. I guess there is
something wrong with the restraint generation. Make sure your residues are
sequentially numbered and in your PDB file the CXM appears right in front for
your HIS without a TER record in between. You should not need LINK records, but
they won't harm (you can use PDB/PDB-REDO entry 1ev5 as an example of the
format).
HTH,
Robbie
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Luca
> Mazzei
> Sent: Friday, May 17, 2019 16:41
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] weight term and geometry
>
> Dear all,
>
> I have a question about how PBDREDO and REFMAC treat the geometry
> weight (gw). In particular, I have a structure with a N-terminal CXM bound to
> a HIS as a second residue. After complete refinement, I run PDBREDO to
> choose the most appropriate gw. Let’s say best results are found using gw =
> 0.1. I run REFMAC using that value, but the carbonyl carbon of CXM detaches
> from the amidic N of HIS (distance 1.84 A). If i run the same job using a gw
> of
> 0.2, 0.3 and so on, that distance decreases and the C-N bond is restored. By
> the way, increasing the gw Rfree increases as well as the difference between
> Rfactor and Rfree.
> Any idea on how to solve the problem? Should I keep higher Rfree and
> worse stats with still having a peptide bond there?
>
> Thank you,
>
> Luca
>
> Luca Mazzei - PhD
> Department of Pharmacy and Biotechnology University of Bologna Viale
> Giuseppe Fanin, 40 - 40127 Bologna - Italy
>
>
>
>
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