NMR Ensembles of Models: Difference between revisions
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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]</ref> and ''NMR in Wikipedia''<ref>[http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR in Wikipedia]</ref>. | 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]</ref> and ''NMR in Wikipedia''<ref>[http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR in Wikipedia]</ref>. | ||
==Display of NMR Models | ==Displaying NMR Models== | ||
===Display of NMR Models by Proteopedia=== | |||
{{STRUCTURE_1lcd| PDB=1lcd | SCENE= }} | {{STRUCTURE_1lcd| PDB=1lcd | SCENE= }} | ||
Proteopedia shows '''all the models''' in ensembles of models from NMR experiments. This enables you to see where the models agree with each other, and where they differ. Each model is shown as a thin backbone trace (a line connecting alpha carbon atoms of amino acids, or phosphorus atoms in DNA or RNA chains). The backbone traces are colored by <font color="blue">'''Amino'''</font> to <font color=" | Proteopedia shows '''all the models''' in ensembles of models from NMR experiments. This enables you to see where the models agree with each other, and where they differ. Each model is shown as a thin backbone trace (a line connecting alpha carbon atoms of amino acids, or phosphorus atoms in DNA or RNA chains). The backbone traces are colored by <font color="blue">'''Amino'''</font> to <font color="red">'''Carboxy'''</font> "rainbow", a spectral sequence of colors starting at the amino terminus (or 5' terminus of nucleic acid chains) and ending at the carboxy terminus (or 3' terminus). | ||
Ligands ([[Hetero atoms]]) are also shown for all models, except that they are opaque only for model 1, and translucent for all other models. Ligand atoms are colored by element, using the [[CPK color scheme]].j | Ligands ([[Hetero atoms]]) are also shown for all models, except that they are opaque only for model 1, and translucent for all other models. Ligand atoms are colored by element, using the [[CPK color scheme]].j | ||
The example at right shows the 3 models for [[1lcd]], a lac repressor domain bound to DNA, with one sodium ion. Water is present in this model but for clarity, Proteopedia does not show water in its initial scene. | The example at right shows the 3 models for [[1lcd]], a lac repressor domain bound to DNA, with one sodium ion. Water is present in this model but for clarity, Proteopedia does not show water in its initial scene. | ||
===Individual Models=== | |||
In order to view individual models, click on ''Jmol'' (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. | |||
===Animating NMR Ensembles=== | |||
When the models in an NMR ensemble are played like a movie, the resulting animation simulates thermal motion (although not all the motions is necessarily real -- see [[below]]). In order to animate the models, click on ''Jmol'' (lower right corner below the molecule) to ''''open Jmol's menu'''. Choose '''Animation''', then '''Animation mode''', and click on '''Loop'''. Then choose ''Animation'' again, and click '''Play'''. You can change the speed of the animation with '''FPS''' (frames per second) on the ''Animation'' menu. By default, there is a delay at the first and last models. | |||
==Multiple Model Ensembles from NMR== | ==Multiple Model Ensembles from NMR== | ||