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ValidatorDB:Database organization

34 bytes added, 07:40, 8 September 2014
Processing Warnings
==Processing Warnings==
[[File:VDB_Warnings.PNG|thumb|right|650px|The '''Processing warnings''' tabof the ''specifics page'' lists unusual circumstances encountered during validation.]]
The validation reports in ValidatorDB ''specifics page'' may also mention various contain the separate tab '''Processing warnings''', which lists unusual aspects circumstances encountered during the validationof each molecule. Sometimes the processed PDB entries contain information that is ambiguous, conflicting or which deviates strongly from the expected reference. [[ValidatorDB]] reports such events as processing warnings. Such information can be found in the  Some '''Processing Warningswarnings''' tab on the specifics page. The selection field at the top of the page helps filter the warnings for different residues, in case more of them are in validation report. Simply click on the drop down menu and select the category of warnings that you would like to explore. Processing warnings are issues that may cause incorrect Validationvalidation, such as bad two residues molecules being too close together in the 3D space, or some atoms being too far (misused concept disconnected) from the rest of alternate conformations) or unusual bond lengths given by the CONECT recordsmolecule. Such structures are generally marked as ''degenerate'' in the ''completeness'' analyses. Make sure that negative Other '''processing warnings''' are only meant to inform of which course of action was taken during validation results (e.g., missing atomswhich conformer was validated if several conformers of that molecule were present in the original PDB entry) are not in fact caused by ignoring some atoms in an ill. The drop down menu at the top of the page helps filter the warnings for molecules with a specific annotation (3-formed structure....include degenerate..letter code).
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