Introduction to molecular visualization: Difference between revisions
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<span style="background-color:black;padding:5px 8px 1px 6px;font-size:140%;"><b><font color="#bbb">C</font> <font color="white">H</font> <font color="red">O</font> <font color="#58f">N</font> <font color="yellow">S</font></b></span> | <span style="background-color:black;padding:5px 8px 1px 6px;font-size:140%;"><b><font color="#bbb">C</font> <font color="white">H</font> <font color="red">O</font> <font color="#58f">N</font> <font color="yellow">S</font></b></span> | ||
</td></tr></table> | </td></tr></table> | ||
Atomic representations (displays, renderings) include '''ball-and-stick, stick (wireframe), and spacefilling'''. The 20 amino acids are [http://biomodel.uah.es/en/model3/aa.htm here represented in each of these 3 ways], and also illustrated in this [[Glycine|page about Glycine]]. These representations show positions of atoms and covalent bonds. Such representations are useful for looking at atomic detail, but become too cluttered to be useful for visualizing [[peptides]] or [[chains|protein chains]]. | Atomic representations (displays, renderings) include '''ball-and-stick, stick (wireframe), and spacefilling'''. The 20 amino acids are [http://biomodel.uah.es/en/model3/aa.htm here represented in each of these 3 ways], and also illustrated in this [[Glycine|page about Glycine]]. These representations show positions of atoms and covalent bonds. [[Hydrogen in macromolecular models|Hydrogen]], shown | ||
in the images at right, is [[Hydrogen in macromolecular models|often missing]] in crystallographic models. Such representations are useful for looking at atomic detail, but become too cluttered to be useful for visualizing [[peptides]] or [[chains|protein chains]]. | |||
''Ball and stick'' is one option in the ''representations'' tab of Proteopedia's [[Scene Authoring Tools]]. Another is ''stick'', also called ''wireframe''. | ''Ball and stick'' is one option in the ''representations'' tab of Proteopedia's [[Scene Authoring Tools]]. Another is ''stick'', also called ''wireframe''. | ||
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{{Clear}} | {{Clear}} | ||
====Disulfide Bonds==== | ====Disulfide Bonds==== | ||
<table | <table class="wikitable" style="text-align:center;margin: 0px 0px 0px 16px;"> | ||
<tr><td width="200"> | |||
[[Image:Ss1.png|200px]] | [[Image:Ss1.png|200px]] | ||
</td><td width="180"> | |||
[[Image:Ss2.png|180px]] | |||
</td><td width="180"> | |||
[[Image:Ss3.png|180px]] | |||
</td><td width="160"> | |||
[[Image:Ss4.png|160px]] | |||
</td><td width="170"> | |||
[[Image:Ss5.png|170px]] | |||
</td></tr><tr><td> | |||
Atomic detail of a between-chain disulfide bond in [[9ins]]. | |||
<span style="background-color:black;padding:5px 8px 1px 6px;font-size:120%;"><b><font color="#bbb">C</font> <font color="red">O</font> <font color="#58f">N</font> <font color="yellow">S</font></b></span> | |||
</td><td> | </td><td> | ||
Protein chains | |||
<span style="background-color:black;padding:5px 8px 1px 6px;font-size:110%;"><b><font color="#acb8e2">A</font> <font color="#a0df99">B</font></b></span> | |||
simplified to backbone traces. | |||
</td><td> | </td><td> | ||
[[FirstGlance in Jmol|FirstGlance]] enlarges the sulfur-sulfur bond. | |||
</td><td> | </td><td> | ||
Schematic disulfide bridge connecting ribbon backbones. | |||
</td><td> | </td><td> | ||
Disulfide bridge colored by chain, an option in [[FirstGlance in Jmol|FirstGlance]]. | |||
</td></tr></table> | </td></tr></table> | ||
[[FirstGlance in Jmol]] highlights disulfide bonds in one click (in its ''Tools'' tab), and has | |||
several options for rendering and coloring them. | |||
{{Clear}} | {{Clear}} | ||
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==Obtaining Molecular Models== | ==Obtaining Molecular Models== | ||
You can browse for molecular models at the [http://atlas.molviz.org Atlas of Macromolecules], the [http://pdb101.rcsb.org/ Molecule of the Month], or [https://web.expasy.org/spotlight/ Protein Spotlight]. | |||
[[How To Find A Structure]] explains an easy way to find a structure for a protein of interest, and how to choose the best one available when there is more than one. [[Empirical models]] are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are the most reliable, but one must pay attention to the [[Quality assessment for molecular models|quality of an empirical model]] since some are more reliable than others. | |||
Empirical models are available for only a small fraction of all proteins, probably <10%. | Empirical models are available for only a small fraction of all proteins, probably <10%. When an empirical model is not available, [[AlphaFold]] has a proven track record of predicting protein structures correctly from their sequences, using artificial intelligence (AI). [[AlphaFold]] also reliably predicts the confidence of each part of a predicted structure. | ||
==See Also== | ==See Also== | ||
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*[[History of Macromolecular Visualization]] | *[[History of Macromolecular Visualization]] | ||
*[[Molecular Sculpture]] | *[[Molecular Sculpture]] | ||
[[Category: Alternate Renderings]] | |||