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PDBsum entry 6eyc
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Nuclear protein
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PDB id
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6eyc
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Contents |
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603 a.a.
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605 a.a.
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641 a.a.
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633 a.a.
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616 a.a.
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689 a.a.
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References listed in PDB file
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Key reference
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Title
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Isolde: a physically realistic environment for model building into low-Resolution electron-Density maps.
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Author
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T.I.Croll.
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Ref.
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Acta Crystallogr D Struct Biol, 2018,
74,
519-530.
[DOI no: ]
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PubMed id
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Abstract
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This paper introduces ISOLDE, a new software package designed to provide an
intuitive environment for high-fidelity interactive remodelling/refinement of
macromolecular models into electron-density maps. ISOLDE combines interactive
molecular-dynamics flexible fitting with modern molecular-graphics visualization
and established structural biology libraries to provide an immersive interface
wherein the model constantly acts to maintain physically realistic conformations
as the user interacts with it by directly tugging atoms with a mouse or haptic
interface or applying/removing restraints. In addition, common validation tasks
are accelerated and visualized in real time. Using the recently described
3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome
maintenance (MCM) helicase complex as a case study, it is demonstrated how
ISOLDE can be used alongside other modern refinement tools to avoid common
pitfalls of low-resolution modelling and improve the quality of the final model.
A detailed analysis of changes between the initial and final model provides a
somewhat sobering insight into the dangers of relying on a small number of
validation metrics to judge the quality of a low-resolution model.
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Secondary reference #1
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Title
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New tool: phenix.Real_space_refine
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Authors
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P.V.Afonine,
J.J.Headd,
T.T.Terwilliger,
P.D.Adams.
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Ref.
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comput cryst newsl, 2013,
4,
43.
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Secondary reference #2
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Title
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Phenix: a comprehensive python-Based system for macromolecular structure solution.
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Authors
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P.D.Adams,
P.V.Afonine,
G.Bunkóczi,
V.B.Chen,
I.W.Davis,
N.Echols,
J.J.Headd,
L.W.Hung,
G.J.Kapral,
R.W.Grosse-Kunstleve,
A.J.Mccoy,
N.W.Moriarty,
R.Oeffner,
R.J.Read,
D.C.Richardson,
J.S.Richardson,
T.C.Terwilliger,
P.H.Zwart.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2010,
66,
213-221.
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PubMed id
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