Introduction to Jmol - Revision history

Eric Martz at 14:31, 1 February 2019

2019-02-01T14:31:43Z

← Older revision		Revision as of 14:31, 1 February 2019
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	~~=== '''Jmol Introduction''' ===~~

	== What is Jmol? ==		== What is Jmol? ==
	Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.		Jmol is a free, open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.
	[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]		[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]
	What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.		What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.

Jaime Prilusky: Sandbox Jmol Introduction moved to Introduction to Jmol

2019-01-31T05:17:56Z

Sandbox Jmol Introduction moved to Introduction to Jmol

← Older revision	Revision as of 05:17, 31 January 2019
(No difference)

Jamie C. Gladfelder at 00:29, 2 July 2013

2013-07-02T00:29:30Z

← Older revision		Revision as of 00:29, 2 July 2013
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	This drug is a good example, because it will allow us to view how the drug is able to fit into a pocket withing the protease. The first scene that we see here is one pulled from RCSB Protein Data Bank.		This drug is a good example, because it will allow us to view how the drug is able to fit into a pocket withing the protease. The first scene that we see here is one pulled from RCSB Protein Data Bank.

			This scene demonstrates the secondary structure of the <scene name='55/552182/Protease/1'>protease</scene>. The ligand and water molecules have been hidden in order to view the protein alone.

			This scene shows the <scene name='55/552182/Pocket/1'>pocket</scene> in which darunavir fits into.

			After inverting the selection and targeting the ligand we can visualize <scene name='55/552182/Darunavir/2'>darunavir</scene>.

	</StructureSection>		</StructureSection>

Jamie C. Gladfelder at 23:52, 1 July 2013

2013-07-01T23:52:38Z

← Older revision		Revision as of 23:52, 1 July 2013
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	What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.		What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.
	[[Image:3ttp.pdb.jpg\|325px\|left\|thumb\| <span style="font-size:1.2em;"></span>]]		[[Image:3ttp.pdb.jpg\|325px\|left\|thumb\| <span style="font-size:1.2em;"></span>]]
			In order to use Jmol you can start from scratch by building your own molecule or you can download one from the RCSB Protein Data Bank.
	== Who uses Jmol? ==		== Who uses Jmol? ==
	Many people use Jmol as an educational, chemistry and biochemistry tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:		Many people use Jmol as an educational, chemistry and biochemistry tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:
	[[http://wiki.jmol.org/index.php/Main_Page]]		[[http://wiki.jmol.org/index.php/Main_Page]]
			<StructureSection load='3ttp' size='350' side='right' caption='Structure of multiresistant HIV-1 protease in complex with darunavir (PDB entry [[3ttp]])' scene=''>

			== Example of Jmol ==
			As an example we will be using the drug darunavir. Darunavir (Prezista) was approved in 2006 for the treatment of HIV-1. Darunavir is a second generation protease inhibitor. Proteases are used during the HIV replication in order to cut proteins the viruses need in order to survive. Protease inhibitors work by "plugging" the protease and not allowing the HIV proteins to be cut; thus, inhibiting HIV synthesis.

			This drug is a good example, because it will allow us to view how the drug is able to fit into a pocket withing the protease. The first scene that we see here is one pulled from RCSB Protein Data Bank.

	~~<StructureSection load='3ttp' size='350' side='right' caption='Structure of multiresistant HIV-1 protease in complex with darunavir (PDB entry [[3ttp]])' scene=''>~~
	~~Anything in this section will appear adjacent to the 3D structure and will be scrollable.~~

	</StructureSection>		</StructureSection>

Jamie C. Gladfelder at 23:33, 1 July 2013

2013-07-01T23:33:39Z

← Older revision		Revision as of 23:33, 1 July 2013
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	[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]		[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]
	What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.		What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.
			[[Image:3ttp.pdb.jpg\|325px\|left\|thumb\| <span style="font-size:1.2em;"></span>]]
	== Who uses Jmol? ==		== Who uses Jmol? ==
	Many people use Jmol as an educational, chemistry and biochemistry tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:		Many people use Jmol as an educational, chemistry and biochemistry tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:

Jamie C. Gladfelder at 23:23, 1 July 2013

2013-07-01T23:23:21Z

← Older revision		Revision as of 23:23, 1 July 2013
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	== Who uses Jmol? ==		== Who uses Jmol? ==
	Many people use Jmol as an educational tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:		Many people use Jmol as an educational, chemistry and biochemistry tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:
	[[http://wiki.jmol.org/index.php/Main_Page]]		[[http://wiki.jmol.org/index.php/Main_Page]]


	<StructureSection load='3ttp' size='350' side='right' caption='Structure of ~~HMG~~-~~CoA reductase~~ (PDB entry [[~~1dq8~~]])' scene=''>		<StructureSection load='3ttp' size='350' side='right' caption='Structure of multiresistant HIV-1 protease in complex with darunavir (PDB entry [[3ttp]])' scene=''>
	Anything in this section will appear adjacent to the 3D structure and will be scrollable.		Anything in this section will appear adjacent to the 3D structure and will be scrollable.

	</StructureSection>		</StructureSection>

Jamie C. Gladfelder at 21:51, 1 July 2013

2013-07-01T21:51:02Z

← Older revision		Revision as of 21:51, 1 July 2013
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	Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.		Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.
	[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]		[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]
			What makes this program very useful is Jmol's ability to manipulate the 3D models and display the molecules as "ball and stick," "space filling," "ribbon," "cartoon," etc. One can also do a combination of any or all possible displays. For example: one can display a ligand as "ball and stick" while displaying the protein its interacting with in a "cartoon" display.

	== Who uses Jmol? ==		== Who uses Jmol? ==

Jamie C. Gladfelder at 21:35, 1 July 2013

2013-07-01T21:35:51Z

← Older revision		Revision as of 21:35, 1 July 2013
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	== What is Jmol? ==		== What is Jmol? ==
	Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.		Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.
			[[Image:Jmol.png\|325px\|right\|thumb\| <span style="font-size:1.2em;"></span>]]

	== Who uses Jmol? ==		== Who uses Jmol? ==

Jamie C. Gladfelder: New page: === '''Jmol Introduction''' === == What is Jmol? == Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but h...

2013-07-01T21:27:52Z

New page: === '''Jmol Introduction''' === == What is Jmol? == Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but h...

New page

=== '''Jmol Introduction''' ===

== What is Jmol? ==
Jmol is an open-source program that allows the viewer to see chemical structures in three dimensions. Jmol previously used Java, but has now switched to HTML5-only.

== Who uses Jmol? ==
Many people use Jmol as an educational tool to help visualize molecules and compounds. Many websites, books and even blogs use Jmol as we can see from this site:
[[http://wiki.jmol.org/index.php/Main_Page]]

<StructureSection load='3ttp' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>