WHAT CHECK program

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... 

These two fiinctionals differ in the form ofthe VWN correlation functional that they use. References in ilic literature to the LSDA functional usually refer to SVWN5, but some earlier references meant SVWN by LSDA. Gaussiatfs L A keyword is a synonym for VWN. However, other DFT programs refer to what Gaussian c s SVWN5 as LSDA. Check program documentation carefully when making o)mparison of various LSDA functionals. For these reasons, we do not use the term LSDA at all. 

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 detail plan for each audit may include dates if it is to cover several days but the main substance of the plan will be what is to be audited, against what requirements, and by whom. At the detail level, the specific requirements to be checked should be identified based upon risks, past performance, and when it was last checked. Overall plans are best presented as program charts and detail plans as checklists. Audit planning should not be taken lightly. Audits require effort from auditees as well as the auditor so a well-planned audit designed to discover pertinent facts quickly is far better than a rambling audit which jumps from area to area looking at this or that without any obvious direction. 

After obtaining the prototypes, tests must be made to determine the utility. Generally these include a short time destructive test to determine the strength and to check out the basic design. Another test that is done is to use the product in the projected environment with stress levels increased in a rational manner to make for an accelerated life test. Other tests may include consumer acceptance tests to determine what instructions in proper use are required, tests for potential safety hazards, electrical tests, self-extinguishing tests, and any others that the product requires. In the case of high risk products, the test program is continued even after the product enters service. 

Whether we have written it informally or in more precise form, we should have a specification of what is expected of each operation. We should attempt to check that the program code of each operation conforms to what is expected of it. 

However, these checking functions are not a bad place to start. Read the Goof-Proof advice for using spell and grammar check in Appendix A at the back of this book. Once you have made the corrections suggested by those programs, you will need to conduct checks of your own. Also, refer back to Rule 32 and review just what a spell checker can and cannot help you with. 

Now it s time to start. Read the Introduction The Five-Step Program Chapter 1, What You Need to Know About the AP Chemistry Exam and Chapter 2, How to Plan Your Time. Then, take the Diagnostic Exam in Chapter 3. Your score will show how well you understand the material right now and point out weak areas that may need a little extra attention. Use the review exams at the end of the chapters to check your comprehension. Also pay attention to the free-response questions. That is where you can really shine, and they are worth almost as much as the multiple-choice part. Use the Rapid Reviews to brush up on the important points in the chapters. Keep this book handy—it is going to be your friend for the next few weeks or months. 

What about Preventive maintenance A preventive maintenance program should be established in consultation with those responsible for the upkeep of the chamber during normal use. This should be done after successful qualification and prior to releasing the chamber for use. Components that are prone to malfunction due to normal wear and tear include solenoid valves, humidifier floats, and recirculation-fan drive motors. These components should be checked or replaced on a regular basis to prevent or minimize chamber downtime. 

The phosphate program contains zinc. What level of zinc is present in the recirculating water (Further double-check on correct addition rate.)... 

After you have a model structure, you should check its reasonableness and completeness. Most programs allow you to use the computer s mouse or touch pad to rotate the model on the computer screen. You should carefully inspect the structure from various orientations and make sure the computer understood what you intended. Some programs do not show double bonds as two lines or do not show aromatic rings with a dotted circle in the center. Hence, you need to make sure the hybridization of the atoms is right, so that phenyl rings are flat, and so on. 

The point of programmed learning is that you learn at your own pace and that you yourself check on your own progress. I shall give you information and ideas in chunks called frames, each numbered and separated by a black line. Most frames contain a question, sometimes followed by a comment or clue, and always by the answer. You must WRITE DOWN on a piece of paper your answer to each question. You ll find that you discover as you do so whether you really see what is being explained or not. If you simply say to yourself Oh,... 

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