Coot Modelbuilding tools for Molecular Graphics分子图形建模工具的傻瓜.pptVIP

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2016-12-30 发布于上海
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Coot Modelbuilding tools for Molecular Graphics分子图形建模工具的傻瓜.ppt

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Structure Validationusing Coot Paul Emsley Stand-alone Tools Coot is designed around a set of libraries Easy to make “Break-out”/Stand-alone validation tools Dynarama Interactive Ramachandran Tool Blob identification tool Density Fit analysis tool B-factor variation tool Nomenclature-fix tool EBI Deposition Validation Tools (GE) “Validation tools used by the EBI are different to Coot tools and give a different set of things about which to be concerned” Is this true? Does it matter? Nomenclature correction Validation: GLN ASN B-factor amino-carbonylo outliers Often difficult to decide on the orientation of the last chi angle of GLNs and ASNs (There is geometry-based validation “clique analysis” in REDUCE) This is a complementary (built-in, faster) density-based validation tool Presumes sensible temperature factor refinement Compares the difference in B-factor of OD1 and ND2 with the standard deviation of the B-factors of the other atoms GLN and ASN B-factor outliers We choose a value of 2.25 sigma to be the cut-off Even in reference structures there are deviations that result from erroneous structures (presumably) Validation futures More/Closer integration with Molprobity Tools Parse REMARKS in Molprobity PDB files Interactive NCS difference graph tool Communication with Refmac Geometric violations Nucleic Acid Validation Not any time soon * * * Mar 2007 York University of York Refinement Validation External e.g. REFMAC Internal Internal External e.g. MolProbity Feature Integration Validation Tools Geometry Distortion Bonds, Angles, Planes B-factor variance Density Fit Peptide Omega angle Water check By distance/map density/B-factor By difference map variance Un-modelled density blobs Molprobity’s Reduce Probe (fix-nomenclature-errors 1) Cut-off for acceptable values Z value Number observed