Clashes: Difference between revisions

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==Clashes vs. Model Quality==

The presence of too many clashes in a model calls its reliability into question. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent), ~~and then~~ determines a clash score ("clashscore"). The clashscore 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 [[wwPDB]] entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref> that includes an analysis of clashes. Here are a couple of examples:

The presence of too many clashes in a model calls its reliability into question. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent), determines a clash score ("clashscore"), and ranks the clashscore relative to other models of the same resolution.. The clashscore is the number of clashes per 1,000 atoms (including hydrogens) 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 [[wwPDB]] entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref> that includes an analysis of clashes. Here are a couple of examples:

* [[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. [https://files.rcsb.org/pub/pdb/validation_reports/zx/6zx4/6zx4_full_validation.pdf Full Validation Report]. Caution: the percentile rank is based on a reference dataset from the time of deposition (or earlier?). 6zx4 was deposited in July, 2020. The validation reference dataset had about 70% of the X-ray entries in the stated resolution range 0.86-1.06 Å that were present in the wwPDB in November, 2021.

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 ==Clashes vs. Model Quality==
-The presence of too many clashes in a model calls its reliability into question. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent), and then determines a clash score ("clashscore"). The clashscore 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 [[wwPDB]] entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref> that includes an analysis of clashes. Here are a couple of examples:
+The presence of too many clashes in a model calls its reliability into question. All models submitted to the Protein Data Bank (PDB) are analyzed by [[MolProbity]], which adds hydrogen atoms (where absent), determines a clash score ("clashscore"), and ranks the clashscore relative to other models of the same resolution.. The clashscore is the number of clashes per 1,000 atoms (including hydrogens) 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 [[wwPDB]] entry has an extensive Validation Report<ref>[https://www.wwpdb.org/validation/validation-reports wwPDB Validation Reports].</ref> that includes an analysis of clashes. Here are a couple of examples:
 * [[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. [https://files.rcsb.org/pub/pdb/validation_reports/zx/6zx4/6zx4_full_validation.pdf Full Validation Report]. Caution: the percentile rank is based on a reference dataset from the time of deposition (or earlier?). 6zx4 was deposited in July, 2020. The validation reference dataset had about 70% of the X-ray entries in the stated resolution range 0.86-1.06 Å that were present in the wwPDB in November, 2021.