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Experimental phasing: Difference between revisions
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== Heavy atoms and their properties == | |||
* Heavy atom choices (includes links to papers) - http://xray0.princeton.edu/~phil/Facility/heavyatompick.html | |||
* Heavy atom Database system (server) - http://hatodas.harima.riken.go.jp/ | |||
* MAD phasing - http://skuld.bmsc.washington.edu/scatter/AS_index.html | |||
== Heavy atom refinement and phasing programs == | == Heavy atom refinement and phasing programs == | ||
* [http://www.globalphasing.com/sharp/ SHARP] | * [[SHARP]] /[http://www.globalphasing.com/sharp/ autoSHARP] | ||
[[SHARP]] was the first "product" of [http://www.globalphasing.com/ Global Phasing], in the mid '90s. It was a spectacular improvement over existing methods and has been described in [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4B432JN-DY&_user=3208271&_coverDate=12%2F31%2F1997&_alid=865881649&_rdoc=5&_fmt=high&_orig=search&_cdi=18066&_sort=d&_docanchor=&view=c&_ct=5&_acct=C000047720&_version=1&_urlVersion=0&_userid=3208271&md5=1a457e261908cb35b80cd39fc7c7cd6d Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods]. | |||
SHARP has been regularly improved since then, and the legendary 'week-long runs' now complete in a few minutes. Much has been argued about how SHARP implements Maximum Likelihood, and Phaser and BP3 claim to do better in SAD cases. SHARP does do really well for SAD phasing, but the main advantage still is the ability to describe very complicated experiments, involving multiple wavelengths, various crystals of the same derivative and various derivatives (all with or without anomalous data) in a very appropriate manner. All these can also be done through the autoSHARP pipeline as well. The SHARP interface is web based, excellent on-line help, and very good examples. | |||
A CCP4i interface to autoSHARP is also available. It should be noted that this is (besides the old MLPHARE) the only program accessible from CCP4i that permits MAD phasing. | |||
* [http://cns-online.org/v1.2/ CNS] | |||
Maximum likelihood phasing in CNS appeared to my recollection shortly after SHARP and has a perfectly decent implementation that has solved many structures and produces excellent maps. It has an excellent web-based interface, good on-line help, and very good example scripts. | |||
* | * [http://solve.lanl.gov/Solve/solve.html SOLVE] | ||
SOLVE was the first truly automated experimental phasing pipeline in the second half of the '90s. Its worth mentioning also in this section, since it uses a number of ingenious solutions to the phasing problem, e.g. correlated phasing, that produce phases of excellent quality and can easily be used just for phasing outside its own pipeline. | SOLVE was the first truly automated experimental phasing pipeline in the second half of the '90s. Its worth mentioning also in this section, since it uses a number of ingenious solutions to the phasing problem, e.g. correlated phasing, that produce phases of excellent quality and can easily be used just for phasing outside its own pipeline. | ||
* | * [http://shelx.uni-ac.gwdg.de/SHELX SHELXE] | ||
SHELXE is again mostly used in the context of the SHELX suite and the HKL2MAP pipeline but is an excellent stand alone solution as well. Its peculiarity is the combination of phasing and density modification tricks in a very quick iterative fashion, and it can produce excellent results. | SHELXE is again mostly used in the context of the SHELX suite and the HKL2MAP pipeline but is an excellent stand alone solution as well. Its peculiarity is the combination of phasing and density modification tricks in a very quick iterative fashion, and it can produce excellent results. | ||