[phenixbb] phenix.rna_validate and the MolProbity web server report different bond angle violations

[Huw Jenkins]

Hi,

I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. 

As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported:

RNA Validation
-----------------------------------------------
Pucker Outliers:
#residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler
   G A  15 :74.054:no:103.458:yes
   U A  48 :119.081:yes:283.965:no
   U A  63 :90.366:yes:74.220:yes

-----------------------------------------------
Bond Length Outliers:
#residue:atom_1:atom_2:num_sigmas

-----------------------------------------------
Angle Outliers:
#residue:atom_1:atom_2:atom_3:num_sigmas
   C A  39 : C5': C4': C3':-5.294
   U A  63 : O3': C3': C2':-4.402

-----------------------------------------------
Suite Outliers:
#suiteID:suite:suiteness:triaged_angle
   G A  16 :!!:0.000:epsilon-1
   U A  48 :!!:0.000:delta
   U A  49 :!!:0.000:delta-1
   A A  64 :!!:0.000:epsilon-1

The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations:

A 39		 C	worst is C5'-C4'-C3': 10.588 σ
A 63		 U	worst is O3'-C3'-C2': 8.803 σ
A 54		 C	worst is C5'-C4'-C3': 7.883 σ
A 49		 U	worst is C2'-C1'-N1: 5.416 σ
A 62		 G	worst is C2'-C1'-N9: 4.946 σ
A 15		 G	worst is O3'-C3'-C2': 4.825 σ
A 22		 U	worst is C5'-C4'-C3': 4.785 σ
A 64		 A	worst is C4'-C3'-O3': 4.648 σ
A 65		 A	worst is C2'-C1'-N9: 4.582 σ
A 44		 A	worst is C4'-C3'-C2': 4.395 σ

As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. 

Hopefully there is a simple explanation!

Thanks,


Huw