On Tue, 2012-01-10 at 13:25 +0000, Luca Pellegrini wrote:
> "This is not a reliable map."
There are many reasons why one could get the gap in R-values. As the
proud author of an "unreliable" map myself (3pht), I found that what did
it was that the TLS-refined model was deposited with the full B-factors
(per PDB reqs). Since the EDS scripts are smart enough to detect the
TLS records and apply them, the R-values were way off. It also did
wanders to the metal ions that were (perhaps mistakenly) not included in
the TLS groups.
Curiously, this often happens to really good high res structures (e.g.
the largest subangstrom structure ever solved, 3ju4 mentioned in the
other thread). I suspect the deal is the software mismatch, as it was
refined with SHELX to R~11%, and without fine-tuning the refmac
refinement one gets R~16%.
Results are often much more consistent at pdb_redo, given that it
actually refines the models. For instance, 3ju4 is reported at R~11%.
The maps look cleaner too.
On a personal note, I must say that I had very positive experience
remediating the 3pht entry at EDS.
Cheers,
Ed.
--
After much deep and profound brain things inside my head,
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs
