[phenixbb] estimated coordinate error from phenix.refine

Almudena Ponce Salvatierra maps.farma at gmail.com
Tue Feb 28 05:50:01 PST 2017

Dear all,

I would like to know how the estimated coordinate error is calculated in
phenix.refine, the one that is written on the pdb file as "ML based".

I'm asking due to the following:

For example if I am comparing two different models (structures determined
at 2.1 and 2 Angstroms) but one does have a coordinate error estimate of
0.25 Angstroms and the other one of 0.6, respectively. Is the first model
more reliable? The second one is reliable too but my question points
towards how conservative or how more conservative should I be when
describing distances , potential H bonds, coordination. Despite those
different numbers in estimated coordinate error, the electron density maps
look very similar or almost the same for both structures, very clear and
complete at 2 Angstroms. That's why I was somehow surprised to find these

Thank you very much in advance



Dr. Almudena Ponce-Salvatierra
EMBL-European Molecular Biology Laboratory
71, avenue des Martyrs - CS 90181
F - 38042 Grenoble Cedex 9
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