Clashes: Difference between revisions

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==Clashes vs. Model Quality==

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 determines a clash score, 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.

==Visualization of Clashes==

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 ==Clashes vs. Model Quality==
-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 determines a clash score, 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.
 ==Visualization of Clashes==