MantisBT - Rosetta | |||||
View Issue Details | |||||
ID | Project | Category | View Status | Date Submitted | Last Update |
0000290 | Rosetta | [All Projects] Incorrect Results | public | 2013-07-09 17:06 | 2013-07-15 10:26 |
Reporter | momeara | ||||
Assigned To | AndrewLeaverFay | ||||
Priority | normal | Severity | major | Reproducibility | always |
Status | resolved | Resolution | fixed | ||
Platform | All platforms | OS | Any | OS Version | Any |
Product Version | Trunk | ||||
Fixed in Version | Trunk | ||||
Application(s) Affected | rosetta_scripts FastRelax standard mover | ||||
Command Line Used | standard rosetta_scripts command line | ||||
Developer Options | Confirmed As Bug | ||||
Fixed in SVN Version | 55496 | ||||
Summary | 0000290: Loss of Density in Heavy Atom Distances of 2.855A | ||||
Description | 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 | ||||
Steps To Reproduce | I see the problem in relax natives | ||||
Additional Information | |||||
Tags | No tags attached. | ||||
Relationships | |||||
Attached Files | ![]() https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=37&type=bug | ||||
Issue History | |||||
Date Modified | Username | Field | Change | ||
2013-07-09 17:06 | momeara | New Issue | |||
2013-07-09 17:06 | momeara | Status | new => assigned | ||
2013-07-09 17:06 | momeara | Assigned To | => AndrewLeaverFay | ||
2013-07-09 17:06 | momeara | File Added: long_dip.zip | |||
2013-07-15 10:26 | AndrewLeaverFay | Fixed in SVN Version | => 55496 | ||
2013-07-15 10:26 | AndrewLeaverFay | Note Added: 0000305 | |||
2013-07-15 10:26 | AndrewLeaverFay | Status | assigned => resolved | ||
2013-07-15 10:26 | AndrewLeaverFay | Fixed in Version | => Trunk | ||
2013-07-15 10:26 | AndrewLeaverFay | Resolution | open => fixed |
Notes | |||||
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