Dear all: I find that phenix.refine reports a higher starting R-free than those stated for structures downloaded from the PDB. For instance, the R-free stated in the PDB = 0.287, using Polygon = 0.2880, but the Start R-free from phenix.refine = 0.3114 Is this usual, or is something seriously wrong? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458
Hi Jerome, can you send a log file? What's the PDB code? Differences in R between published and recomputed values are expected but in this case it is strange that Polygon and phenix.refine report different values since they use the same routines to compute them. Pavel. On 5/9/11 1:12 PM, Jerome Nwachukwu wrote:
Dear all: I find that phenix.refine reports a higher starting R-free than those stated for structures downloaded from the PDB. For instance, the R-free stated in the PDB = 0.287, using Polygon = 0.2880, but the Start R-free from phenix.refine = 0.3114 Is this usual, or is something seriously wrong? Thank you, -Jerome
On Mon, May 9, 2011 at 1:19 PM, Pavel Afonine
Differences in R between published and recomputed values are expected but in this case it is strange that Polygon and phenix.refine report different values since they use the same routines to compute them.
If hydrogens were added prior to refinement, this could explain the gap. -Nat
participants (3)
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Jerome Nwachukwu -
Nathaniel Echols -
Pavel Afonine