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Difference density maps are usually calculated using
Fourier coefficients which are the differences between the observed structure factor amplitudes from the X-ray diffraction experiment and the calculated structure factor amplitudes from the current model, using the phase from the model for both
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224:
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The use of ML weighting reduces model bias (due to using the model's phase) in the 2 Fo–Fc map, which is the main estimate of the true density. However, it does not fully eliminate such bias.
412:" scale factor. These coefficients are derived from the gradient of the likelihood function of the observed structure factors on the basis of the current model. A difference map built with
47:
with positive density—electron density where there's nothing in the model, usually corresponding to some constituent of the crystal that hasn't been modelled, for example a
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55:-- in green, and negative density—parts of the model not backed up by electron density, indicating either that an atom has been disordered by
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It is now normal to also include maximum-likelihood weighting terms which take into account the estimated errors in the current model:
68:
terms (since no phases are available for the observed data). The two sets of structure factors must be on the same scale.
576:
Terwilliger, TC; Grosse-Kunstleve, RW; Afonine, PV; Moriarty, NW; Adams, PD; Read, RJ; Zwart, PH; Hung, LW (May 2008).
59:
or that it is modelled in the wrong place—in red. The typical contouring (display threshold) is set at 3σ.
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578:"Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias"
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Yamashita, Keitaro; Palmer, Colin M.; Burnley, Tom; Murshudov, Garib N. (1 October 2021).
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467:"Cryo-EM single-particle structure refinement and map calculation using Servalcat"
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386:{\displaystyle C_{diffmap}=(m|F_{obs}|-D|F_{calc}|)exp(2\pi i\phi _{calc})}
441:
219:{\displaystyle C_{diffmap}=(|F_{obs}|-|F_{calc}|)exp(2\pi i\phi _{calc})}
32:
of the crystal and the electron density explained by the current model.
529:"You are lost without a map: Navigating the sea of protein structures"
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shows the spatial distribution of the difference between the measured
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which is an estimate of the cosine of the error in the phase, and
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Biochimica et
Biophysica Acta (BBA) - Proteins and Proteomics
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A way to compute this map has been formulated for cyro-EM.
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527:Lamb, AL; Kappock, TJ; Silvaggi, NR (April 2015).
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442:"RCSB PDB: X-ray Electron Density Maps"
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43:Conventionally, they are displayed as
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420:is known as a mFo – DFc map.
545:10.1016/j.bbapap.2014.12.021
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602:10.1107/S0907444908004319
492:10.1107/S2059798321009475
440:Bank, RCSB Protein Data.
53:crystallisation adjutant
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22:difference density map
637:Electron density maps
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18:X-ray crystallography
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594:2008AcCrD..64..515T
483:2021AcCrD..77.1282Y
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477:(10): 1282–1291.
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30:electron density
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449:. Retrieved
446:www.rcsb.org
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408:is a "σ
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641:Proteopedia
63:Calculation
45:isosurfaces
451:2021-01-08
427:References
363:ϕ
356:π
303:−
196:ϕ
189:π
139:−
26:Fo–Fc map
650:Category
620:18453687
563:25554228
511:34605431
611:2424225
590:Bibcode
554:5051661
502:8489229
479:Bibcode
39:Display
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396:where
49:ligand
400:is a
51:or a
616:PMID
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537:1854
507:PMID
416:and
20:, a
639:on
606:PMC
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24:or
16:In
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418:D
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350:(
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107:=
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80:C
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