About: Puzzle 438   Sponge Permalink

An Entity of Type : owl:Thing, within Data Space : dbkwik.org associated with source dataset(s)

Puzzle 438 Electron density Puzzle1 foldit_1310497228.png|438 start irc_33153_1310569528.png|after alignment irc_104378_1310568068 enzyme.png|after alignment irc_235191_1310567976 gramps.png|438 gramps advice irc_235191_1310768315 gramps method.png|438 gramps method irc_12518_1311116511 The GUmmer evolver VC.png|438 The GUmmer spmm evolver VC irc_12518_1311116487 the GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116563 The GUmme evlover VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116908 The GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_188194_1311116920 jermainiac.png|438 jermainiac irc_188194_1311117512 jermainiac.png|438 jermainiac irc_174969_1311116679 rav3n_pl start at guide.png|438 rav3n_pl start as guide irc_174969_1311116993 rav3n_pl.png|438 r

AttributesValues
rdfs:label
  • Puzzle 438
rdfs:comment
  • Puzzle 438 Electron density Puzzle1 foldit_1310497228.png|438 start irc_33153_1310569528.png|after alignment irc_104378_1310568068 enzyme.png|after alignment irc_235191_1310567976 gramps.png|438 gramps advice irc_235191_1310768315 gramps method.png|438 gramps method irc_12518_1311116511 The GUmmer evolver VC.png|438 The GUmmer spmm evolver VC irc_12518_1311116487 the GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116563 The GUmme evlover VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116908 The GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_188194_1311116920 jermainiac.png|438 jermainiac irc_188194_1311117512 jermainiac.png|438 jermainiac irc_174969_1311116679 rav3n_pl start at guide.png|438 rav3n_pl start as guide irc_174969_1311116993 rav3n_pl.png|438 r
dcterms:subject
abstract
  • Puzzle 438 Electron density Puzzle1 foldit_1310497228.png|438 start irc_33153_1310569528.png|after alignment irc_104378_1310568068 enzyme.png|after alignment irc_235191_1310567976 gramps.png|438 gramps advice irc_235191_1310768315 gramps method.png|438 gramps method irc_12518_1311116511 The GUmmer evolver VC.png|438 The GUmmer spmm evolver VC irc_12518_1311116487 the GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116563 The GUmme evlover VC.png|438 The GUmmer Spmm evolver VC irc_12518_1311116908 The GUmmer evolver VC.png|438 The GUmmer Spmm evolver VC irc_188194_1311116920 jermainiac.png|438 jermainiac irc_188194_1311117512 jermainiac.png|438 jermainiac irc_174969_1311116679 rav3n_pl start at guide.png|438 rav3n_pl start as guide irc_174969_1311116993 rav3n_pl.png|438 rav3n_pl irc_215720_1311117163 pauldunn.png|438 paul dunn irc_215720_1311117180 pauldunn.png|438 paul dunn foldit_1311123690.png|438 BootsMcGraw 3rd place solo foldit_1311123704.png|438 BootsMcGraw 3rd place solo foldit_1311123722.png|438 BootsMcGraw 3rd place solo 3LUR.pdb1.jpg|3LUR pdb jmol image 3LUR.pdb12.png|3LUR pdb jmol 243 Mark in green native in blue.jpg|234 Mark in green native in blue Puzzle # 438, Electron Density 1, was the first puzzle to use the concept of electron density as a guide for players. Electron density is the measure of the probability of an electron being present at a specific location. Density was presented as a map with adjustable tolerances, the smaller the tolerance, the more likely the protein might conform to the native structure, if matched to fall within the density boundaries. Like Quest To The Native and similar puzzles, the object is to match the guide as closely as possible. Unlike QTTNs, the actual structure of the protein is unknown. BootsMcGraw, scoring 11940 for a third place finish, started this puzzle by first manually rebuilding the loops to fall within the density map as closely as possible. Once the structure more or less matched the guide, Boots turned off the guide and set in place one of the many Quake-style compressor scripts until the score stopped increasing. At this point, one of the auto-rebuild scripts was implemented until it stopped yielding points. The resulting structure was compared to the guide, and more manual rebuilding and compression was done until no more points were found. The puzzle was then walked for a few more points. Gramps method: Banding to this Electron Density cloud was quite an adventure. Here are some rough and ready tips from my first pass: 1. use initial alignment and don't touch the Move Tool until banding complete 2. Band from one structure at a time, doing the easy cases first and then using these as aids to interpolation for the hard ones. Protein 3LUR in RCSB PDB in NCBI
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