Clashes: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 9: | Line 9: | ||
The presence of too many clashes in a model calls into question its reliability. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent). MolProbity then determines a clash score ("clashscore"), which is the number of clashes per 1,000 atoms (including hydrogens), and ranks it relative to other models of the same resolution. A clash is considered to occur when the van der Waals radii overlap by ≥ 0.4 Å<ref>[https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts Too-Close Contacts] at the World Wide Protein Data Bank.</ref>. Each PDB entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref>. Here are a couple of examples: | The presence of too many clashes in a model calls into question its reliability. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent). MolProbity then determines a clash score ("clashscore"), which is the number of clashes per 1,000 atoms (including hydrogens), and ranks it relative to other models of the same resolution. A clash is considered to occur when the van der Waals radii overlap by ≥ 0.4 Å<ref>[https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts Too-Close Contacts] at the World Wide Protein Data Bank.</ref>. Each PDB entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref>. Here are a couple of examples: | ||
* [[6ef8]], a cryo-EM model, contains 22,911 non-hydrogen atoms. MolProbity added 20,895 hydrogens for a total of 43,806 atoms. 558 clashes were present with atomic overlaps in the range 0.4 to 1.47 Å. The clashscore is thus 558/43.8 = 13. This placed it in about the 35th percentile among the clashscores for all cryo-EM models. | * [6zx4]], an X-ray model of resolution 0.96 Å, contains 5,850 atoms including hydrogens. 6 clashes were present with atomic overlaps in the range 0.41-0.49 Å. The clashscore is thus 6/5.8 = 1.0. This placed it in about the 90th percentile (90% of the compared models have more clashes) of 1,321 models with resolutions of 0.86-1.06 Å. | ||
* [[6ef8]], a cryo-EM model of resolution 3.7 Å, contains 22,911 non-hydrogen atoms. MolProbity added 20,895 hydrogens for a total of 43,806 atoms. 558 clashes were present with atomic overlaps in the range 0.4 to 1.47 Å. The clashscore is thus 558/43.8 = 13. This placed it in about the 35th percentile (35% of the compared models have more clashes) among the clashscores for all cryo-EM models. | |||
==Visualization of Clashes== | ==Visualization of Clashes== | ||
