ValidatorDB:Database contents - Revision history

Lukas at 15:11, 10 August 2015

2015-08-10T15:11:34Z

← Older revision		Revision as of 15:11, 10 August 2015
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	'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] and [[ValidatorDB:Principles \| ~~principles~~]] ~~governing ValidatorDB before you read this page. Once you become familiar with the type of content you may expect to find in ValidatorDB, have a look at how this content is~~ [[~~ValidatorDB~~:~~Database_organization~~ \| ~~organized~~]]~~.'''~~		'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] of MotiveValidator and ValidatorDB and principles governing [[ValidatorDB:Principles \| ValidatorDB]] or [[MotiveValidator:Principles \| MotiveValidator]] before you read this page

	For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in each ''validated molecule'' to those in the corresponding ''model''. '''ValidatorDB''' ~~reports~~ correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''. The results of the ''advanced'' analyses are reported as ''warnings''. Additionally, unusual circumstances encountered during validation are reported separately as ''processing warnings''.		For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in each ''validated molecule'' to those in the corresponding ''model''. '''ValidatorDB''' and '''MotiveValidator''' report correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''. The results of the ''advanced'' analyses are reported as ''warnings''. Additionally, unusual circumstances encountered during validation are reported separately as ''processing warnings''.

	In '''ValidatorDB''', the results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.		In '''ValidatorDB''' and '''MotiveValidator''', the results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.

	__TOC__		__TOC__
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	==Wrong chirality==		==Wrong chirality==
	'''ValidatorDB''' ~~presents~~ the results of several kinds of ''chirality'' analyses. If an issue is found, the following types of results are reported:		'''ValidatorDB''' and '''MotiveValidator''' present the results of several kinds of ''chirality'' analyses. If an issue is found, the following types of results are reported:
	** '''Wrong chirality (Carbon)''': the chirality error was found on an sp3 hybridized carbon atom.		** '''Wrong chirality (Carbon)''': the chirality error was found on an sp3 hybridized carbon atom.
	** '''Wrong chirality (Planar)''': the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.		** '''Wrong chirality (Planar)''': the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.
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	[[File:VDB warnings.png\|thumb\|right\|700px\| Examples of ''warnings'' reported during the ''advanced'' analyses.]]		[[File:VDB warnings.png\|thumb\|right\|700px\| Examples of ''warnings'' reported during the ''advanced'' analyses.]]

	Aside from the ''completeness'' and ''chirality'' analyses, '''ValidatorDB''' also ~~performs~~ a set of ''advanced'' analyses. These are meant to bring attention to aspects which may be indicators of further problems in the structure, or, on the contrary, explain why some errors were found during the ''completeness'' and ''chirality'' analyses. For example, if a molecule is part of a polymer, a reported change in chirality might be a consequence of some glitch in the polymer building process. Of course, each situation should be studied individually, but the ''advanced'' analyses provide a good starting point.		Aside from the ''completeness'' and ''chirality'' analyses, '''ValidatorDB''' and '''MotiveValidator''' also perform a set of ''advanced'' analyses. These are meant to bring attention to aspects which may be indicators of further problems in the structure, or, on the contrary, explain why some errors were found during the ''completeness'' and ''chirality'' analyses. For example, if a molecule is part of a polymer, a reported change in chirality might be a consequence of some glitch in the polymer building process. Of course, each situation should be studied individually, but the ''advanced'' analyses provide a good starting point.

	When issues are found during an ''advanced'' analysis, a warning is reported:		When issues are found during an ''advanced'' analysis, a warning is reported:
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	Aside from the results of the ''completeness'', ''chirality'' and ''advanced'' analyses, '''ValidatorDB''' also provides a list of all unusual circumstances encountered during validation in the form of '''processing warnings'''. Typically, the '''processing warnings''' provide information about why a molecule marked as ''degenerate'' could not be validated, which conformer was used if more conformers were available in the original PDB entry (either in the form of alternate rotamers, or multiple NMR models), etc.		Aside from the results of the ''completeness'', ''chirality'' and ''advanced'' analyses, '''ValidatorDB''' also provides a list of all unusual circumstances encountered during validation in the form of '''processing warnings'''. Typically, the '''processing warnings''' provide information about why a molecule marked as ''degenerate'' could not be validated, which conformer was used if more conformers were available in the original PDB entry (either in the form of alternate rotamers, or multiple NMR models), etc.

	'''Continue by learning about the [[ValidatorDB:Database_organization \| ~~organization~~]] ~~of ValidatorDB,~~ or ~~return to the~~ [[~~ValidatorDB~~:~~UserManual~~ \| ~~Table of contents~~]].'''		'''Continue by learning about the organization of [[ValidatorDB:Database_organization \| ValidatorDB]] or [[MotiveValidator:Service_Organization \| MotiveValidator]].'''

Crina: /* Processing warnings */

2014-10-20T22:16:03Z

Processing warnings

← Older revision		Revision as of 22:16, 20 October 2014
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	=Processing warnings=		=Processing warnings=
	Aside from the results of the ''completeness'', ''chirality'' and ''advanced'' analyses, '''ValidatorDB''' also provides a list of all unusual circumstances encountered during validation in the form of '''processing warnings'''. Typically, the '''processing warnings''' provide information about why a molecule marked as ''degenerate'' could not be validated, which conformer was used if more conformers were available in the original PDB entry (either in the form of alternate rotamers, or multiple NMR models), etc.		Aside from the results of the ''completeness'', ''chirality'' and ''advanced'' analyses, '''ValidatorDB''' also provides a list of all unusual circumstances encountered during validation in the form of '''processing warnings'''. Typically, the '''processing warnings''' provide information about why a molecule marked as ''degenerate'' could not be validated, which conformer was used if more conformers were available in the original PDB entry (either in the form of alternate rotamers, or multiple NMR models), etc.

			'''Continue by learning about the [[ValidatorDB:Database_organization \| organization]] of ValidatorDB, or return to the [[ValidatorDB:UserManual \| Table of contents]].'''

Crina at 21:04, 20 October 2014

2014-10-20T21:04:01Z

← Older revision		Revision as of 21:04, 20 October 2014
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	'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] and [[ValidatorDB:Principles \| principles]] governing ValidatorDB before you read this page.'''		'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] and [[ValidatorDB:Principles \| principles]] governing ValidatorDB before you read this page. Once you become familiar with the type of content you may expect to find in ValidatorDB, have a look at how this content is [[ValidatorDB:Database_organization \| organized]].'''

	For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in each ''validated molecule'' to those in the corresponding ''model''. '''ValidatorDB''' reports correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''. The results of the ''advanced'' analyses are reported as ''warnings''. Additionally, unusual circumstances encountered during validation are reported separately as ''processing warnings''.		For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in each ''validated molecule'' to those in the corresponding ''model''. '''ValidatorDB''' reports correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''. The results of the ''advanced'' analyses are reported as ''warnings''. Additionally, unusual circumstances encountered during validation are reported separately as ''processing warnings''.

Crina: /* Processing warnings */

2014-09-08T10:29:10Z

Processing warnings

← Older revision		Revision as of 10:29, 8 September 2014
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	=Processing warnings=		=Processing warnings=
	~~Furthermore~~, ~~for each~~ validation ~~run, there is~~ '''~~Processing~~ warnings''' ~~tab available, where one can find warnings about the processed structures~~. Typically, ~~there is an information about skipped~~ ''~~alternate conformation residues~~'', ''~~wrong CONNECT records~~'' ~~from the parent PDB file,~~ ''~~processed models'' (~~in ~~case~~ the ~~parent~~ PDB ~~is composed of multiple models) etc. Finally, as a general rule,~~ in the ~~validation interface~~, ~~errors are marked in <span style="color:#FF0000">red</span> (missing atoms)~~ or ~~<span style="color:#DAA520">dark yellow</span> (wrong chirality~~), ~~correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>~~.		Aside from the results of the ''completeness'', ''chirality'' and ''advanced'' analyses, '''ValidatorDB''' also provides a list of all unusual circumstances encountered during validation in the form of '''processing warnings'''. Typically, the '''processing warnings''' provide information about why a molecule marked as ''degenerate'' could not be validated, which conformer was used if more conformers were available in the original PDB entry (either in the form of alternate rotamers, or multiple NMR models), etc.

Crina: /* Warnings */

2014-09-08T10:24:49Z

Warnings

← Older revision		Revision as of 10:24, 8 September 2014
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	=Warnings=		=Warnings=
	[[File:VDB warnings.png\|thumb\|right\|700px\| ''~~'ValidatorDB'~~'' ~~also reports warnings in~~ the ~~complete structures such as ''substitutions'', ''different naming'' or~~ ''~~foreign atoms~~''.]]		[[File:VDB warnings.png\|thumb\|right\|700px\| Examples of ''warnings'' reported during the ''advanced'' analyses.]]

	* '''Substitution''': An atom from the validated ~~motif~~ is of a different chemical element than the corresponding atom in the model ~~residue~~ (e.g. O mapped to N). This happens often at linkage sites.		Aside from the ''completeness'' and ''chirality'' analyses, '''ValidatorDB''' also performs a set of ''advanced'' analyses. These are meant to bring attention to aspects which may be indicators of further problems in the structure, or, on the contrary, explain why some errors were found during the ''completeness'' and ''chirality'' analyses. For example, if a molecule is part of a polymer, a reported change in chirality might be a consequence of some glitch in the polymer building process. Of course, each situation should be studied individually, but the ''advanced'' analyses provide a good starting point.
	* '''Different naming''': An atom from the validated ~~motif~~ has a different PDB atom name than the corresponding atom from the model ~~residue~~ (e.g. the C1 atom mapped to the C7 atom). This happens often when the original PDB files were produced by different software.
	* '''Foreign atom''': An atom from the model ~~residue~~ was mapped to an atom from outside the validated ~~residue~~ (i.e. from its surroundings).		When issues are found during an ''advanced'' analysis, a warning is reported:
	* '''Alternate conformations''': In the original PDB file, the validated ~~residue~~ contains atoms which were given ~~in conformations~~ (i.e., most probably different rotamers). Only the first ~~rotamer~~ was considered during validation.		* '''Substitution''': An atom from the validated molecule is of a different chemical element than the corresponding atom in the model (e.g. O from the model is mapped to N from the validated molecule). This happens often at linkage sites for ligands which are covalently bound to biomolecules.
	* '''Zero model RMSD''': The superimposition between the model ~~residue~~ and the validated ~~motif~~ has a root mean square deviation of zero, i.e., the validated ~~motif~~ is identical to the model ~~residue~~ used as reference.		* '''Different naming''': An atom from the validated molecule has a different PDB atom name than the corresponding atom from the model (e.g. the C1 atom from the model is mapped to the C7 atom from the validated molecule). This happens often when the original PDB files were produced by different software.
			* '''Foreign atom''': An atom from the model was mapped to an atom from outside the validated molecule (i.e. from its surroundings). This happens often at linkage sites for polymeric ligands or ligands which are covalently bound to biomolecules.
			* '''Alternate conformations''': In the original PDB file, the validated molecule contains at least some parts (some or all atoms) for which alternate conformers were given (i.e., most probably different rotamers). Only the first conformer was considered during validation.
			* '''Zero model RMSD''': The superimposition between the model and the validated molecule has a root mean square deviation of zero, i.e., the validated molecule is identical to the model used as reference.

	While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.		While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.

Crina: /* Complete structures */

2014-09-08T10:11:49Z

Complete structures

← Older revision		Revision as of 10:11, 8 September 2014
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	[[File:VDB chirality.png\|thumb\|right\|400px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]		[[File:VDB chirality.png\|thumb\|right\|400px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]

	~~Complete~~ validated ~~structures include~~ all the atoms which are present in the model ~~residue. However, there are still possible issues and warnings can be raised:..~~.''Chirality'' is evaluated only for ~~the~~ complete ~~structures~~, ~~since~~ the absence of some atoms ~~makes~~ it difficult to check the chirality ~~of some~~ of the remaining atoms.		If no issue was found during the ''completeness'' analyses, the validated molecule is marked as ''complete'', because it contains all the atoms which are present in the model. ''Chirality'' is further evaluated only for these molecules with ''complete structure'', because the absence of some atoms can make it difficult to check the chirality of the remaining atoms.

	==Wrong chirality==		==Wrong chirality==
	* '''~~Wrong chirality~~'''~~: an atom from~~ the ~~validated motif has different~~ chirality ~~than~~ the ~~corresponding atom from the model residue. This category can be further specified by identifying a source~~ of ~~the chirality issue.~~		'''ValidatorDB''' presents the results of several kinds of ''chirality'' analyses. If an issue is found, the following types of results are reported:
	** '''~~C atom~~''': the chirality error was found on ~~a single bonded~~ carbon atom.		** '''Wrong chirality (Carbon)''': the chirality error was found on an sp3 hybridized carbon atom.
	** '''Planar ~~atom~~''': the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.		** '''Wrong chirality (Planar)''': the chirality error was found on a planar chiral center. Because of their spacial distribution, planar chiral centers are very sensitive even to small perturbations in the position of the substituents. Therefore, some of the errors reported here might not be significant.
	** '''Metal ~~atom~~''': the chirality error was found on a metal chiral center.		** '''Wrong chirality (Metal)''': the chirality error was found on a metal chiral center.
	** '''High order ~~atom~~''': the chirality error was detected on an atom, ~~which~~ is ~~bonded with~~ a bond of higher order ~~than one. A typical example is phosphorus~~.		** '''Wrong chirality (High order)''': the chirality error was detected on a chiral atom (e.g., phosphorus) where at least one substituent is bound by a bond of higher order.
	** '''Other''': Additional chirality issue which could not be ~~asserted to~~ any of the above categories, ~~for example~~ chirality issues on ~~Nitrogen~~.		** '''Other''': Additional chirality issue which could not be listed in any of the above categories (e.g., chirality issues on nitrogen atoms). These appear rarely in the Protein Data Bank (<0.5% of molecules).

			If any issue is detected on any atom during any ''chirality'' analysis, the molecule is marked as having ''wrong chirality'', because there is at least one atom in the validated molecule with different chirality than the corresponding atom in the model. If more atoms in a molecule exhibit the same type of chirality issue, the validated molecule is counted only once in each type of statistics (e.g., if 3 carbon atoms in one glucose molecule have wrong chirality, this glucose molecule will contribute only once to the statistics on "wrong chirality (carbon)"). If a validated molecule exhibits issues in more than one type of ''chirality'' analysis, it will be counted once in each corresponding statistics (e.g., heme molecules may appear both in the statistics for ''wrong chirality (planar)'', and for the ''wrong chirality (metal)'').

	==Correct chirality==		==Correct chirality==
	If no issues are detected during the ''~~Chirality~~'' analyses, the validated molecule is marked as having ''~~Correct chirality~~'~~', whereas the remaining molecules are marked as having ''Wrong~~ chirality''~~. When issues are found during an~~ '~~'Advanced'' analysis~~, ~~a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations. Each type of issue encountered during validation has a specific color code.~~		If no issues are detected during the ''chirality'' analyses, the validated molecule is marked as having '''correct chirality''', because it contains all atoms present in the model, and each of these atoms has the same chirality in the validated molecule and in the model.

	Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model ~~from wwPDB CCD. Further~~, ~~an error in high order chirality often marks the involvement~~ of ~~phosphate O~~ atoms in ~~salt or ester formation, or merely a different PDB format identification of phosphate O atoms of~~ the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.

	~~The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner~~ in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.

	~~Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e~~. ~~Planar and Metal, which is often case of ''HEM'' residues)~~

			Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having '''correct chirality (tolerant)'''.
	<br style="clear:both" />		<br style="clear:both" />

Crina at 08:14, 8 September 2014

2014-09-08T08:14:13Z

← Older revision		Revision as of 08:14, 8 September 2014
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	'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] and [[ValidatorDB:Principles \| principles]] governing ValidatorDB before you read this page.'''		'''Please make sure to go through the [[ValidatorDB:Terminology \| terms]] and [[ValidatorDB:Principles \| principles]] governing ValidatorDB before you read this page.'''

	For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in ~~the~~ validated ~~molecules~~ to those in the model. '''ValidatorDB''' reports correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. Additionally, ~~all~~ unusual circumstances encountered during validation are reported as ''warnings''.		For each molecule, the validation report contains several types of results, based on how the molecule fared during the various [[ValidatorDB:Principles#Validation_analyses \| validation analyses ]]. The evaluation relies on comparing all atoms and bonds in each ''validated molecule'' to those in the corresponding ''model''. '''ValidatorDB''' reports correct structures, as well as all potential issues found during validation, namely structures that are wrong either because they are incomplete (missing atoms or rings), or because the chirality of some atoms is incorrect. If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''. The results of the ''advanced'' analyses are reported as ''warnings''. Additionally, unusual circumstances encountered during validation are reported separately as ''processing warnings''.

	~~Note that~~ '''ValidatorDB''' ~~uses a~~ unified color scheme		In '''ValidatorDB''', the results for different types of validation analyses are labeled using the unified color scheme: <span style="color:#006400">complete structure and correct chirality</span>, <span style="color:#FF0000">incomplete structure</span>, <span style="color:#DAA520">wrong chirality</span>, <span style="color:#607d8b">warning</span>.

	~~If no issues are found during the ''completeness'' and ''chirality'' analyses, the molecule is marked as having ''complete structure and correct chirality''.~~		__TOC__

	[[File:VDB incomplete.png\|thumb\|center\|1100px\| Potential issues found during the ''completeness'' analyses. All ''incomplete structures'' are marked in <span style="color:#FF0000">red</span> highlight]]

	~~Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''.~~

	=Incomplete structures=		=Incomplete structures=
			Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''. ''Incomplete structures'' refer to molecules which lack some atoms, or whose structure is significantly distorted in comparison to the model:
	Incomplete structures refer to molecules which lack some atoms, or whose structure is significantly distorted in comparison to the model:
	* '''Missing atoms''': An atom in the model has no corresponding atom in the validated molecule.		* '''Missing atoms''': An atom in the model has no corresponding atom in the validated molecule.
	* '''Missing rings''': At least one missing atom originates from cycles (rings). The formal distinction between ring atoms and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in molecules containing rings, especially where atom identifiers are not useful.		* '''Missing rings''': At least one missing atom originates from cycles (rings). The formal distinction between ring atoms and non-ring atoms (simply denoted as atoms) is meant to allow a quick localization of potential issues in molecules containing rings, especially where atom identifiers are not useful.
	* '''Degenerate''': The molecules could not be validated due to their distorted structure, i.e. significant discrepancies between the atoms and inter-atomic bonds in the validated molecule and in the model. This generally happens when residues are overlapping in the 3D space, or some atoms appear disconnected from the rest of the structure.		* '''Degenerate''': The molecules could not be validated due to their distorted structure, i.e. significant discrepancies between the atoms and inter-atomic bonds in the validated molecule and in the model. This generally happens when residues are overlapping in the 3D space, or some atoms appear disconnected from the rest of the structure.

			[[File:VDB incomplete.png\|thumb\|center\|1100px\| Potential issues found during the ''completeness'' analyses. All ''incomplete structures'' are marked in <span style="color:#FF0000">red</span> highlight]]

	=Complete structures=		=Complete structures=
	[[File:VDB chirality.png\|thumb\|right\|~~500px~~\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]		[[File:VDB chirality.png\|thumb\|right\|400px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]

	Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:...''Chirality'' is evaluated only for the complete structures, since the absence of some atoms makes it difficult to check the chirality of some of the remaining atoms.		Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:...''Chirality'' is evaluated only for the complete structures, since the absence of some atoms makes it difficult to check the chirality of some of the remaining atoms.

			==Wrong chirality==
	* '''Wrong chirality''': an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.		* '''Wrong chirality''': an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.
	** '''C atom''': the chirality error was found on a single bonded carbon atom.		** '''C atom''': the chirality error was found on a single bonded carbon atom.
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	** '''Other''': Additional chirality issue which could not be asserted to any of the above categories, for example chirality issues on Nitrogen.		** '''Other''': Additional chirality issue which could not be asserted to any of the above categories, for example chirality issues on Nitrogen.

			==Correct chirality==
	If no issues are detected during the ''Chirality'' analyses, the validated molecule is marked as having ''Correct chirality'', whereas the remaining molecules are marked as having ''Wrong chirality''. When issues are found during an ''Advanced'' analysis, a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations. Each type of issue encountered during validation has a specific color code.		If no issues are detected during the ''Chirality'' analyses, the validated molecule is marked as having ''Correct chirality'', whereas the remaining molecules are marked as having ''Wrong chirality''. When issues are found during an ''Advanced'' analysis, a warning is reported: Substitution, Foreign atom, Different naming, Zero RMSD or Alternate conformations. Each type of issue encountered during validation has a specific color code.

	Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.		Some types of chirality errors do not constitute real issues, but are artifacts of the automated chirality determination procedure. Specifically, an error in planar chirality may just mean that the chiral atom is situated slightly above or below the plane compared to its equivalent in the model from wwPDB CCD. Further, an error in high order chirality often marks the involvement of phosphate O atoms in salt or ester formation, or merely a different PDB format identification of phosphate O atoms of the validated molecule compared to the model. Therefore, if the validated molecule is found to have planar or high order chirality errors, but no other type of chirality issues, the molecule is marked as having ''Correct chirality (tolerant)''.

	~~While the results of the~~ ''~~Advanced~~'' ~~analyses have no bearing over the chemical soundness of~~ the validated ~~molecules, they indicate that further~~, ~~especially automated processing of these structures can be very problematic. Comparison between~~ the ~~structures of molecules with~~ the ~~same annotation (3-letter code) from different PDB entries might even be impossible~~ in the ~~presence~~ of ~~a substitution, as~~ the ~~corresponding~~ atoms ~~have different chemical elements~~. ~~PDB atom names cannot be used straightforwardly~~, since ~~even element symbols can differ and atoms can~~ be ~~formally included in neighboring residues~~.		The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.

	Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of ''HEM'' residues)		Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of ''HEM'' residues)

	* '''~~Uncertain chirality~~''': the ~~presence of unusual bonds may cause an improper evaluation of chirality~~.		<br style="clear:both" />

			=Warnings=
			[[File:VDB warnings.png\|thumb\|right\|700px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]

	* '''Substitution''': An atom from the validated motif is of a different chemical element than the corresponding atom in the model residue (e.g. O mapped to N). This happens often at linkage sites.		* '''Substitution''': An atom from the validated motif is of a different chemical element than the corresponding atom in the model residue (e.g. O mapped to N). This happens often at linkage sites.
	* '''Different naming''': An atom from the validated motif has a different PDB atom name than the corresponding atom from the model residue (e.g. the C1 atom mapped to the C7 atom). This happens often when the original PDB files were produced by different software.		* '''Different naming''': An atom from the validated motif has a different PDB atom name than the corresponding atom from the model residue (e.g. the C1 atom mapped to the C7 atom). This happens often when the original PDB files were produced by different software.
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	* '''Zero model RMSD''': The superimposition between the model residue and the validated motif has a root mean square deviation of zero, i.e., the validated motif is identical to the model residue used as reference.		* '''Zero model RMSD''': The superimposition between the model residue and the validated motif has a root mean square deviation of zero, i.e., the validated motif is identical to the model residue used as reference.

	~~The last category~~ '''~~Correct chirality~~'~~'' includes all~~ the validated ~~residues~~, ~~where all~~ the ~~atoms~~ from ~~the validated motif have a matching partner~~ in the ~~model structure and the chirality~~ of the ~~chiral~~ atoms ~~is correct~~. ~~Last but not least~~, ~~additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar'''~~ and ~~'''High order''' since these might not~~ be ~~significant~~.		While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.

			<br style="clear:both" />

	=Processing warnings=		=Processing warnings=
	Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.		Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.

	~~[[File:VDB warnings.png\|thumb\|left\|1000px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]~~

Crina at 06:56, 8 September 2014

2014-09-08T06:56:22Z

← Older revision		Revision as of 06:56, 8 September 2014
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	Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''.		Validated molecules exhibiting an error in at least one of the ''Completeness'' analyses are denoted as ''incomplete'', whereas the remaining molecules are reported as ''complete''.

	==Incomplete structures==		=Incomplete structures=

	Incomplete structures refer to molecules which lack some atoms, or whose structure is significantly distorted in comparison to the model:		Incomplete structures refer to molecules which lack some atoms, or whose structure is significantly distorted in comparison to the model:
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	* '''Degenerate''': The molecules could not be validated due to their distorted structure, i.e. significant discrepancies between the atoms and inter-atomic bonds in the validated molecule and in the model. This generally happens when residues are overlapping in the 3D space, or some atoms appear disconnected from the rest of the structure.		* '''Degenerate''': The molecules could not be validated due to their distorted structure, i.e. significant discrepancies between the atoms and inter-atomic bonds in the validated molecule and in the model. This generally happens when residues are overlapping in the 3D space, or some atoms appear disconnected from the rest of the structure.

	==Complete structures==		=Complete structures=
	[[File:VDB chirality.png\|thumb\|right\|500px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]		[[File:VDB chirality.png\|thumb\|right\|500px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]

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	While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.		While the results of the ''Advanced'' analyses have no bearing over the chemical soundness of the validated molecules, they indicate that further, especially automated processing of these structures can be very problematic. Comparison between the structures of molecules with the same annotation (3-letter code) from different PDB entries might even be impossible in the presence of a substitution, as the corresponding atoms have different chemical elements. PDB atom names cannot be used straightforwardly, since even element symbols can differ and atoms can be formally included in neighboring residues.





	Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of ''HEM'' residues)		Note that in case a validated residues belongs to more than one category, it can be found in all of them (i.e. Planar and Metal, which is often case of ''HEM'' residues)
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	The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.		The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.

	==Processing warnings==		=Processing warnings=
	Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.		Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.

	[[File:VDB warnings.png\|thumb\|left\|1000px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]		[[File:VDB warnings.png\|thumb\|left\|1000px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]

Crina at 06:53, 8 September 2014

2014-09-08T06:53:30Z

← Older revision		Revision as of 06:53, 8 September 2014
Line 51:		Line 51:
	The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.		The last category '''Correct chirality''' includes all the validated residues, where all the atoms from the validated motif have a matching partner in the model structure and the chirality of the chiral atoms is correct. Last but not least, additional category '''Correct (Tolerant) chirality''' further includes motifs with identified chirality issues as '''Planar''' and '''High order''' since these might not be significant.

			==Processing warnings==
	Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.		Furthermore, for each validation run, there is '''Processing warnings''' tab available, where one can find warnings about the processed structures. Typically, there is an information about skipped ''alternate conformation residues'', ''wrong CONNECT records'' from the parent PDB file, ''processed models'' (in case the parent PDB is composed of multiple models) etc. Finally, as a general rule, in the validation interface, errors are marked in <span style="color:#FF0000">red</span> (missing atoms) or <span style="color:#DAA520">dark yellow</span> (wrong chirality), correct structures in <span style="color:#228B22">green</span>, and warnings in <span style="color:#008B8B">cyan</span>.

	[[File:VDB warnings.png\|thumb\|left\|1000px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]		[[File:VDB warnings.png\|thumb\|left\|1000px\| '''ValidatorDB''' also reports warnings in the complete structures such as ''substitutions'', ''different naming'' or ''foreign atoms''.]]

Crina: /* Complete structures */

2014-09-05T11:16:42Z

Complete structures

← Older revision		Revision as of 11:16, 5 September 2014
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	[[File:VDB chirality.png\|thumb\|right\|500px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]		[[File:VDB chirality.png\|thumb\|right\|500px\| Complete structures can contain chirality issues on a variety of different atom types, here all possible cases occuring in '''ValidatorDB''' are illustrated.]]

	Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:		Complete validated structures include all the atoms which are present in the model residue. However, there are still possible issues and warnings can be raised:...''Chirality'' is evaluated only for the complete structures, since the absence of some atoms makes it difficult to check the chirality of some of the remaining atoms.

	* '''Wrong chirality''': an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.		* '''Wrong chirality''': an atom from the validated motif has different chirality than the corresponding atom from the model residue. This category can be further specified by identifying a source of the chirality issue.