[phenixbb] riding model and deposition

Alex Theodossis Alex.Theodossis at med.monash.edu.au
Wed Feb 17 17:44:57 PST 2010

Dear phenixbb,

I have refined a 1.3A structure using individual anisotropic B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding model during refinement has improvement the R values (Rf, 14.5%; Rfree, 16.6%), although bond length and angle outliers did increase (anyone know why that would be?).

I have decided to deposit the model obtained using the riding model, but am unsure whether to include the hydrogen coordinates in the deposition.

The Phenix.refine documentation advises that they are left in, as they are needed to reproduce the  refinement statistics. However, reviewing the high resolution structures in the PDB I found that:

1. In the case of structures refined using REFMAC or SHELX, the riding model does not seem to be included, although its use during refinement is mentioned in the pdb header.

2. In the case of structures refined using PHENIX, use of the riding model is sometimes indicated in the header, but hydrogen coordinates only appear to be included in the pdb in the case of structures refined to a resolution better than 1.3A.

As far as I can understand the purpose of the riding model is to provide additional restraints for refinement, so as long as its use is made evident in the pdb header (and maybe the methods section of the publication) that should be enough. Inclusion of hydrogens in the model, when you can't see them seems inappropriate.
Nevertheless, I would appreciate a more authoritative perspective on this issue.

Thank you in advance,

Alex Theodossis

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