Hi Nat The PDBe used to do the conversion automatically (likely still does) After submission they would send you something like this:
The PDB no longer accepts or releases entries that contain only residual B-factors. For this reason your entry was converted to full B-factors and ANISOU records encoding the TLS parameters using the protocol as given in:
http://deposit.rcsb.org/adit/REFMAC.html
The converted file was then run against EDS refinement and as no change was observed in the calculated R-factors, this was considered for release.
Best R On 16 Dec 2011, at 16:11, Nathaniel Echols wrote:
On Fri, Dec 16, 2011 at 7:54 AM, Da Duan <[email protected]> wrote:
I was just looking at the average B in the refinement log files from Refmac and Phenix Refine. Thanks for the clarification on how Refmac and Phenix calculate the average B. My next question is when depositing the structure, is it more common to deposit structures with the "residual" B-factors or B-factors generated by Phenix that includes the TLS and Ucryst contribution? I also performed sfcheck and the average B generated by the Wilson plot is ~100 which seems to suggest that the Phenix average B is probably "more" correct?
I had thought that the PDB automatically converted Refmac PDB files to contain full B-factors, but the link Ed posted suggests otherwise. If you are depositing the output file from Phenix, at least, you do not need to take any additional steps.
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