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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