MantisBT - Rosetta
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0000290Rosetta[All Projects] Incorrect Resultspublic2013-07-09 17:062013-07-15 10:26
momeara 
AndrewLeaverFay 
normalmajoralways
resolvedfixed 
All platformsAnyAny
Trunk 
Trunk 
rosetta_scripts FastRelax standard mover
standard rosetta_scripts command line
Confirmed As Bug
55496
0000290: Loss of Density in Heavy Atom Distances of 2.855A
There seems to be a loss of density at heavy atom distances of 2.855A (At least HBonding heavy atom Acceptor - Donor distances). It seems to be caused by one of these flags:
    -corrections::chemical:icoor_05_2009
    -analytic_etable_evaluation
    -use_bicubic_interpolation
    -dun10
    -set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.85 fa_standard:NH2O:LK_DGFREE:-7.8 fa_standard:Narg:LK_DGFREE:-10.0 fa_standard:OH:LK_DGFREE:-6.70

It is apparent in bb->bb and sc->sc hbonds so my guess is that it is caused by a concave derivative discontinuity in the analytic_etable evaluation code.


Evidence: for plots, see attached tar.gz

  
For Talaris2013 (trunk) energy function, For Asp/Glu -> Lys hbonds:
     top8000 relaxed natives with no energy function flags
     O->N distance distribution with a tight kernel shows a striking loss of density at 2.855A
          Talaris2013_CXL_AMO_hbond_ADdist_130709.pdf
     O->N vs O->H scatter plot, shows the loss is correlated with the O->N distance
          hbond_geo_dim_pairs_scatter_ADdist_AHdist_chem_type_Talaris2013_130709.pdf

Score12 energy function, backbone->backbone hbonds:
      top8000 relaxed natives with flags:
           -restore_pre_talaris_2013_behavior
      O->N distance distribution with tight kernel zoomed in shows no loss of density at 2.855A
           hbond_ADdist_bb_bb_zoom_Score12_130709.pdf

Baseline energy function, backbone->backbone hbonds:
      top8000 relaxed natives with flags:
          -restore_pre_talaris_2013_behavior
          -corrections::chemical:icoor_05_2009
          -analytic_etable_evaluation
          -use_bicubic_interpolation
          -dun10
          -set_atom_properties fa_standard:ONH2:LK_DGFREE:-5.85 fa_standard:NH2O:LK_DGFREE:-7.8 fa_standard:Narg:LK_DGFREE:-10.0 fa_standard:OH:LK_DGFREE:-6.70
            <s weights=score12prime>
                <Reweight scoretype=fa_sol weight=0.75/>
                                                                                                                                                                                                                
                This was mistakenly set to 0.575 which is not .5 * 1.17
                <Reweight scoretype=hbond_sr_bb weight=0.585/>
                                                                                                                                                                                                                
                Enable the new disf
                <Reweight scoretype=dslf_ss_dst weight=0/>
                <Reweight scoretype=dslf_cs_ang weight=0/>
                <Reweight scoretype=dslf_ss_dih weight=0/>
                <Reweight scoretype=dslf_ca_dih weight=0/>
                <Reweight scoretype=dslf_fa13 weight=1.0/>
        </s>
      O->N distance distribution with tight kernel zoomed in shows loss of density at 2.855A
           hbond_ADdist_bb_bb_zoom_Baseline_130709.pdf
       
I see the problem in relax natives
No tags attached.
zip long_dip.zip (231,129) 2013-07-09 17:06
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=37&type=bug
Issue History
2013-07-09 17:06momearaNew Issue
2013-07-09 17:06momearaStatusnew => assigned
2013-07-09 17:06momearaAssigned To => AndrewLeaverFay
2013-07-09 17:06momearaFile Added: long_dip.zip
2013-07-15 10:26AndrewLeaverFayFixed in SVN Version => 55496
2013-07-15 10:26AndrewLeaverFayNote Added: 0000305
2013-07-15 10:26AndrewLeaverFayStatusassigned => resolved
2013-07-15 10:26AndrewLeaverFayFixed in Version => Trunk
2013-07-15 10:26AndrewLeaverFayResolutionopen => fixed

Notes
(0000305)
AndrewLeaverFay   
2013-07-15 10:26   
https://github.com/RosettaCommons/main/compare/5e4b5398ab...234478ca15 [^]