Introduction to molecular visualization: Difference between revisions
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</td><td> | </td><td> | ||
Protein chains | Protein chains | ||
<span style="background-color:black;padding:5px 8px 1px 6px;font-size: | <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. | simplified to backbone traces. | ||
</td><td> | </td><td> | ||
[[FirstGlance in Jmol|FirstGlance]] enlarges the sulfur-sulfur bond. | [[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]. | |||
Empirical models are available for only a small fraction of all proteins, probably <10%. | [[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%. 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]] | |||