Introduction to molecular visualization - Revision history

Eric Martz at 01:47, 8 March 2025

2025-03-08T01:47:45Z

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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).
	~~__NOTOC__~~
	==Representations of Molecular Models==		==Representations of Molecular Models==
	===Atomic Representations===		===Atomic Representations===

Eric Martz: /* Obtaining Molecular Models */

2024-12-04T19:43:45Z

Obtaining Molecular Models

← Older revision		Revision as of 19:43, 4 December 2024
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	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].		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.		[[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.		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.

Eric Martz: /* Obtaining Molecular Models */

2024-12-04T19:43:17Z

Obtaining Molecular Models

← Older revision		Revision as of 19:43, 4 December 2024
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	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].		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. ''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.		[[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.		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.

Eric Martz: /* Obtaining Molecular Models */

2024-12-04T19:42:25Z

Obtaining Molecular Models

← Older revision		Revision as of 19:42, 4 December 2024
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	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].		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].

	~~Methods for searching the~~ [[~~Protein Data Bank~~]] for ~~published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F\|explained here]]~~. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are ~~far more~~ reliable ~~than [[theoretical models]]~~, but one must pay attention to the [[Quality assessment for molecular models\|quality of an empirical model]] since some are more reliable than others.		[[How To Find A Structure]] explains an easy way to find a structure for a protein of interest. ''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%. If an empirical model is not available, ~~the next best thing would be a~~ [[~~homology model~~]]~~. About one third~~ of ~~all proteins can be reliably homology modeled~~, ~~but homology models have~~ [[~~Practical_Guide_to_Homology_Modeling#Limitations_of_Homology_Modeling\|more uncertainties~~]] ~~than do empirical models~~.		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==

Karsten Theis at 17:02, 10 February 2021

2021-02-10T17:02:16Z

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	*[[History of Macromolecular Visualization]]		*[[History of Macromolecular Visualization]]
	*[[Molecular Sculpture]]		*[[Molecular Sculpture]]
			[[Category: Alternate Renderings]]

Eric Martz: /* Obtaining Molecular Models */

2019-03-07T17:36:28Z

Obtaining Molecular Models

← Older revision		Revision as of 17:36, 7 March 2019
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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]		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].

	Methods for searching the [[Protein Data Bank]] for published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F\|explained here]]. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are far more reliable than [[theoretical models]], but one must pay attention to the [[Quality assessment for molecular models\|quality of an empirical model]] since some are more reliable than others.		Methods for searching the [[Protein Data Bank]] for published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F\|explained here]]. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are far more reliable than [[theoretical models]], but one must pay attention to the [[Quality assessment for molecular models\|quality of an empirical model]] since some are more reliable than others.

Eric Martz: /* Obtaining Molecular Models */

2019-03-07T17:24:46Z

Obtaining Molecular Models

← Older revision		Revision as of 17:24, 7 March 2019
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	==Obtaining Molecular Models==		==Obtaining Molecular Models==
	Methods for searching the [[Protein Data Bank]] for published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F\|explained here]]. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or ~~cryo-~~electron ~~microscopy~~. Empirical models are far more reliable than [[theoretical models]], but one must pay attention to the [[Quality assessment for molecular models\|quality of an empirical model]] since some are more reliable than others.		You can browse for molecular models at the [http://atlas.molviz.org Atlas of Macromolecules]

			Methods for searching the [[Protein Data Bank]] for published empirical 3D models are [[Practical_Guide_to_Homology_Modeling#Do_you_need_a_homology_model.3F\|explained here]]. ''Empirical models'' are those determined by experimentation, notably [[X-ray diffraction]], [[solution nuclear magnetic resonance]], or [[electron cryomicroscopy]]. Empirical models are far more reliable than [[theoretical models]], 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%. If an empirical model is not available, the next best thing would be a [[homology model]]. About one third of all proteins can be reliably homology modeled, but homology models have [[Practical_Guide_to_Homology_Modeling#Limitations_of_Homology_Modeling\|more uncertainties]] than do empirical models.		Empirical models are available for only a small fraction of all proteins, probably <10%. If an empirical model is not available, the next best thing would be a [[homology model]]. About one third of all proteins can be reliably homology modeled, but homology models have [[Practical_Guide_to_Homology_Modeling#Limitations_of_Homology_Modeling\|more uncertainties]] than do empirical models.

Eric Martz: /* Disulfide Bonds */

2018-08-28T19:40:13Z

Disulfide Bonds

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	[[FirstGlance in Jmol\|FirstGlance]] enlarges the sulfur-sulfur bond.		[[FirstGlance in Jmol\|FirstGlance]] enlarges the sulfur-sulfur bond.
	</td><td>		</td><td>
	Schematic disulfide ~~bond~~ connecting ribbon backbones.		Schematic disulfide bridge connecting ribbon backbones.
	</td><td>		</td><td>
	Disulfide ~~bond~~ colored by chain, an option in [[FirstGlance in Jmol\|FirstGlance]].		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

Eric Martz: /* Disulfide Bonds */

2018-08-28T19:39:23Z

Disulfide Bonds

← Older revision		Revision as of 19:39, 28 August 2018
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	Schematic disulfide bond connecting ribbon backbones.		Schematic disulfide bond connecting ribbon backbones.
	</td><td>		</td><td>
	Disulfide bond colored by chain.		Disulfide bond 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

Eric Martz: /* Disulfide Bonds */

2018-08-28T19:38:16Z

Disulfide Bonds

← Older revision		Revision as of 19:38, 28 August 2018
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	</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:~~110~~%;"><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:~~120~~%;"><b><font color="#acb8e2">A</font> <font color="#a0df99">B</font></b></span>		<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>