WHAT CHECK

Knowing what checks have been made using the instrument since it was last checked, so that you can repeat them should the instrument be subsequently found out of calibration - this is only necessary for instruments whose accuracy drifts over time, i.e. electronic equipment. (It is not normally necessary for mechanical devices. You will need a traceability system for this purpose.)... 

WHAT CHECK www.sander.embl-heidelberg.de/whatcheck/ Hooft et al. (1996)... 

Side chain atom packing of amino acid residues has been an important structural quality measure in X-ray.112,113 The structural quality criteria are also introduced for NMR structure quality checks.50,114 However, almost, all NMR structures deposited in PDB uniformly have poor scores for the side chain packing. There is no consensus whether X-ray packing-derived structural criteria can be used for NMR quality check. Some checking programs are available in PDB, e.g., PROCHECK,115 PROCHECK-NMR,116 and WHAT-CHECK.117... 

Hooft et al. [27] described a procedure to extract a representative subset of high-quality structures from the PDB. Since this publication, the PDB has grown by almost a factor of three. Consequently, we can now use more strict selection criteria. The criteria for being acceptable to the WHAT CHECK internal database in 2002 are listed below ... 

There is less than 30% sequence identity to any other protein in the WHAT CHECK database. 

For several years, the European Community (EC) has sponsored a structure validation project. The results of this project are available as a WWW-based server http //biotech.ebi.ac.uk 8400/). The server incorporates PROVE [32] by the Wodak group, PROCHECK by the Thornton group, and WHAT CHECK. 

The validation of alternate atom locations has opened a Pandora s box of its own. The number of errors that crystallographers can make when depositing structures with alternate locations is truly mind-boggling. We only recently started working in WHAT CHECK on the detection of errors in alternate atom indicators. To our... 

The course of the WHAT CHECK structural Z-scores throughout the past 10 years is depicted in Fig. 5. In this analysis, we determined several global Z-scores for all the structures solved in the past 10 years with a resolution between 1.8 and 2.2 A, by using the internal WHAT CHECK database generated in 2000. It can be seen from Fig. 5 that the chi-1/chi-2 rotamer distribution, in particular, has improved over the years, which is most likely due to the use of side-chain conformation libraries in structure determination. The other structural Z-scores show an insignificantly small... 

Figure 5 Average WHAT CHECK structural Z-scores for structures solved at a resolution between 1.8 and 2.2 A. The average Z-scores for the first-generation packing quality are marked by circles, those for the Ramachandran plot appearance by diamonds, those for the chi-1 /chi-2 rotamer distribution by upright triangles and those for the backbone conformation with inverted triangles.

WHAT CHECK CMBI swift.cmbi.ru. nl/gv/ whatcheck/ 4... 

The unit cell parameters have to he known accurately to allow the measurements of distances on an absolute scale. Inaccuracies typically originate from errors in the values for the wavelength of the radiation used for the experiment (for synchrotron data) or from incorrect values for the distance between the crystal and the detector. Programs such as WHAT CHECK (Hooft et al 1996) are available to detect such problems and to suggest corrected values of the unit cell parameters. When the unit cell parameters have been corrected, the structure must be adjusted to the new unit cell by some cycles of refinement. 

WHAT CHECK structure validation program (Hooft et al, 1996) checks approximately 40 different features of a protein s geometry. These checks are aimed at catching all levels of errors, from the careless omission of a protein molecule in the asymmetric unit to the subtle nuances of side chain atom nomenclature. It is easy to get lost in the volumes of information output hy WHAT CHECK. Special attention should he devoted to the following three key checks. 

The detailed plaiming of engineering quality management is a matter of procedures deciding what checks, reviews, and audits will be made, how they will be made, and when they will be made. The quality system may have to comply with the requirements of standards such as the IS09000 series, or the plant owner s stipulations. A few general principles to bear in mind are the following. 

Could the waste generate peroxides and if so what checks/ safeguards are carried out as protection against possible incidents Is the waste stored on hard standing ... 

What checks are carried out by the waste disposal company to ensure that the waste sent off site meets legal requirements ... 

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