<div dir="ltr">It took us a while to figure out what was supposed to happen here, but the answer is that phenix.rna_validate is outdated and the numbers in MolProbity are correct. I'm fixing rna_validate now (and incorporating it into the new phenix.molprobity framework).<div>
<br></div><div>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 13, 2014 at 6:23 AM, Huw Jenkins <span dir="ltr"><<a href="mailto:h.t.jenkins@me.com" target="_blank">h.t.jenkins@me.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
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.<br>
<br>
As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported:<br>
<br>
RNA Validation<br>
-----------------------------------------------<br>
Pucker Outliers:<br>
#residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler<br>
G A 15 :74.054:no:103.458:yes<br>
U A 48 :119.081:yes:283.965:no<br>
U A 63 :90.366:yes:74.220:yes<br>
<br>
-----------------------------------------------<br>
Bond Length Outliers:<br>
#residue:atom_1:atom_2:num_sigmas<br>
<br>
-----------------------------------------------<br>
Angle Outliers:<br>
#residue:atom_1:atom_2:atom_3:num_sigmas<br>
C A 39 : C5': C4': C3':-5.294<br>
U A 63 : O3': C3': C2':-4.402<br>
<br>
-----------------------------------------------<br>
Suite Outliers:<br>
#suiteID:suite:suiteness:triaged_angle<br>
G A 16 :!!:0.000:epsilon-1<br>
U A 48 :!!:0.000:delta<br>
U A 49 :!!:0.000:delta-1<br>
A A 64 :!!:0.000:epsilon-1<br>
<br>
The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations:<br>
<br>
A 39 C worst is C5'-C4'-C3': 10.588 σ<br>
A 63 U worst is O3'-C3'-C2': 8.803 σ<br>
A 54 C worst is C5'-C4'-C3': 7.883 σ<br>
A 49 U worst is C2'-C1'-N1: 5.416 σ<br>
A 62 G worst is C2'-C1'-N9: 4.946 σ<br>
A 15 G worst is O3'-C3'-C2': 4.825 σ<br>
A 22 U worst is C5'-C4'-C3': 4.785 σ<br>
A 64 A worst is C4'-C3'-O3': 4.648 σ<br>
A 65 A worst is C2'-C1'-N9: 4.582 σ<br>
A 44 A worst is C4'-C3'-C2': 4.395 σ<br>
<br>
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.<br>
<br>
Hopefully there is a simple explanation!<br>
<br>
Thanks,<br>
<br>
<br>
Huw<br>
<br>
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</blockquote></div><br></div>