Introduction to molecular visualization: Difference between revisions
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''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ''Molecular visualization'' means looking at molecular models in order to explore and understand them. Molecular visualization does not necessarily involve ''molecular modeling'', which means creating molecular models, or changing the composition or configurations of existing models. Here we will be dealing primarily with models of macromolecules (protein, DNA, RNA, or their complexes). | ||
==Representations of Molecular Models== | ==Representations of Molecular Models== | ||
===Atomic Representations=== | ===Atomic Representations=== | ||
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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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<tr><td width="200"> | <tr><td width="200"> | ||
[[Image:Ss1.png|200px]] | [[Image:Ss1.png|200px]] | ||
</td><td> | </td><td width="180"> | ||
[[Image:Ss2.png| | [[Image:Ss2.png|180px]] | ||
</td><td> | </td><td width="180"> | ||
[[Image:Ss3.png| | [[Image:Ss3.png|180px]] | ||
</td><td> | </td><td width="160"> | ||
[[Image:Ss4.png| | [[Image:Ss4.png|160px]] | ||
</td><td> | </td><td width="170"> | ||
[[Image:Ss5.png| | [[Image:Ss5.png|170px]] | ||
</td></tr><tr><td> | </td></tr><tr><td> | ||
Atomic detail of a between-chain disulfide bond in [[9ins]]. | 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> | <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 | 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 | [[FirstGlance in Jmol|FirstGlance]] enlarges the sulfur-sulfur bond. | ||
</td><td> | </td><td> | ||
Schematic disulfide | Schematic disulfide bridge connecting ribbon backbones. | ||
</td><td> | </td><td> | ||
Disulfide | 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 | [[FirstGlance in Jmol]] highlights disulfide bonds in one click (in its ''Tools'' tab), and has | ||
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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]] | |||
