NMR Ensembles of Models: Difference between revisions
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==Structure Determination by NMR== | ==Structure Determination by NMR== | ||
About | About 6% of the entries in the [[Protein Data Bank]] were determined by nuclear magnetic resonance in solution (NMR) as of October 2024. 83% were determined by [[X-ray crystallography]], 10% by [[electron cryomicroscopy]], and <1% by other methods. NMR can only be used for relatively small macromolecules (see [[#Median_Size_of_Published_NMR_Structures|below]]). | ||
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Model building for NMR experiments typically starts with the complete protein or nucleic acid chain, including [[Hydrogen in macromolecular models|hydrogen atoms]]. The distance restraints are then applied. The resulting model usually includes the entire protein and nucleic acid chains, unlike [[X-ray crystallography|X-ray crystallographic]] models that often lack the ends, and even loops in the middle of chains, due to [[Disorder|disorder]] in protein crystals. | Model building for NMR experiments typically starts with the complete protein or nucleic acid chain, including [[Hydrogen in macromolecular models|hydrogen atoms]]. The distance restraints are then applied. The resulting model usually includes the entire protein and nucleic acid chains, unlike [[X-ray crystallography|X-ray crystallographic]] models that often lack the ends, and even loops in the middle of chains, due to [[Disorder|disorder]] in protein crystals. | ||
Macromolecular structure determination by NMR is done in aqueous solution, and thus requires that the molecule be soluble. For more information, see ''Nature of 3D Structural Data''<ref>[http://www.pdb.org/pdb/static.do?p=general_information/about_pdb/nature_of_3d_structural_data.html Nature of 3D Structural Data | Macromolecular structure determination by NMR is done at high protein concentrations in aqueous solution, and thus requires that the molecule be highly soluble. For more information, see ''NMR in Wikipedia''<ref>[http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR in Wikipedia]</ref> | ||
and ''Nature of 3D Structural Data at PDB''<ref>[https://web.archive.org/web/20110415074813/http://www.pdb.org/pdb/static.do?p=general_information/about_pdb/nature_of_3d_structural_data.html Nature of 3D Structural Data (archived copy)]</ref>. | |||
==Displaying NMR Models== | ==Displaying NMR Models== | ||
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===Individual Models=== | ===Individual Models=== | ||
Proteopedia shows only the first model by default, while it says ''Displaying simplified model''. After you click the <font color="orange">orange '''load full'''</font> button, all models will be displayed. | |||
In order to view individual models, click on ''JSmol'' or ''Jmol_S'' (lower right corner below the molecule) to '''open Jmol's menu'''. There, use the '''All N models''' item (where N is the total number of models in the ensemble). For example, clicking on 1.1: 1 will display only model 1, and the menu will now say ''model 1/N''. You can also use Jmol's menu to change the rendering and coloring. | In order to view individual models, click on ''JSmol'' or ''Jmol_S'' (lower right corner below the molecule) to '''open Jmol's menu'''. There, use the '''All N models''' item (where N is the total number of models in the ensemble). For example, clicking on 1.1: 1 will display only model 1, and the menu will now say ''model 1/N''. You can also use Jmol's menu to change the rendering and coloring. | ||
[[FirstGlance in Jmol]] also shows model 1 by default, but you can click on ''View All Models''. | |||
===Animating NMR Ensembles=== | ===Animating NMR Ensembles=== | ||
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==See Also== | ==See Also== | ||
*[[X-ray crystallography]] | *[[X-ray crystallography]] | ||
*[[Empirical models]] | |||
==References and Websites== | ==References and Websites== | ||
