Jmol/Using the console - Revision history

Karsten Theis at 14:50, 31 October 2020

2020-10-31T14:50:58Z

← Older revision		Revision as of 14:50, 31 October 2020
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	<scene name='86/862210/Ammonia/2'>Ammonia with lone pair cartoon</scene>		<scene name='86/862210/Ammonia/2'>Ammonia with lone pair cartoon</scene>

			<scene name='86/864093/Water/1'>electrostatic potential of water</scene>

	===Electron density===		===Electron density===
			The way electron density is usually shown is as surface, but it warrants its own category because getting the electron density data is a special topic (also discussed at [[User:Karsten Theis/Electron density]].


	===Superpositions===		===Superpositions===

Karsten Theis at 14:29, 31 October 2020

2020-10-31T14:29:52Z

← Older revision		Revision as of 14:29, 31 October 2020
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	===Surfaces===		===Surfaces===
			The "isosurface" command in Jmol draws all kind of surfaces (molecular surface, electron density, orbitals) with all kinds of coloring options (by atom, electrostatic potential, conservation, distance, etc.). It is a complex command, so examples help to learn how to use it.

			<scene name='86/862210/Ammonia/2'>Ammonia with lone pair cartoon</scene>

	===Electron density===		===Electron density===

Karsten Theis at 13:36, 31 October 2020

2020-10-31T13:36:52Z

← Older revision		Revision as of 13:36, 31 October 2020
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	Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn.		Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn.

	Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].		Here is an example, <scene name='78/786673/Gal_overal_view/2'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].

	<jmol><jmolButton><text>zoom in</text><script>moveto 1.0 { 752 -659 33 153.48} 738.33 0.0 0.0 {-32.029 70.295 112.187} 53.8932808874789 {0 0 0} 0 0 0 3.0 0.0 0.0;</script></jmolButton></jmol>		<jmol><jmolButton><text>zoom in</text><script>moveto 1.0 { 752 -659 33 153.48} 738.33 0.0 0.0 {-32.029 70.295 112.187} 53.8932808874789 {0 0 0} 0 0 0 3.0 0.0 0.0;</script></jmolButton></jmol>
	</StructureSection>		</StructureSection>

Karsten Theis at 13:30, 31 October 2020

2020-10-31T13:30:04Z

← Older revision		Revision as of 13:30, 31 October 2020
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	Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].		Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].

			<jmol><jmolButton><text>zoom in</text><script>moveto 1.0 { 752 -659 33 153.48} 738.33 0.0 0.0 {-32.029 70.295 112.187} 53.8932808874789 {0 0 0} 0 0 0 3.0 0.0 0.0;</script></jmolButton></jmol>
	</StructureSection>		</StructureSection>

Karsten Theis at 13:26, 31 October 2020

2020-10-31T13:26:41Z

← Older revision		Revision as of 13:26, 31 October 2020
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	select selected or carbohydrate		select selected or carbohydrate
	wireframe on		wireframe on

			Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn.

	Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].		Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].

	</StructureSection>		</StructureSection>

Karsten Theis at 13:24, 31 October 2020

2020-10-31T13:24:00Z

← Older revision		Revision as of 13:24, 31 October 2020
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	Model 2.1 gets moved and model 1.1 stays in place.		Model 2.1 gets moved and model 1.1 stays in place.

	Here is an example, <scene name='78/786673/Gal_nagal_other_superposition/1'>GAL and NAGAL superimposed via the ligand</scene>. The Jmol script for the scene is here (see Figure X), and the key command is:		Here is an example, <scene name='78/786673/Gal_nagal_other_superposition/1'>GAL and NAGAL superimposed via the ligand</scene>. The Jmol script for the scene is here (see [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Figure X]), and the key command is:

	"compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"		"compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"

Karsten Theis at 13:21, 31 October 2020

2020-10-31T13:21:06Z

← Older revision		Revision as of 13:21, 31 October 2020
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	===Superpositions===		===Superpositions===
	For a superposition, you load a file that contains multiple models, or a structure with multiple copies of the same chain in the asymmetric unit. The example below is for multiple models, with model 1.1 and 2.1 sufficiently similar to be meaningfully superimposed. The three dots ("...") in the two select statements should be filled in such that equivalent atoms are selected. In the example scene below, both structures bind to the same ligand.		For a [[Jmol/superposition]], you load a file that contains multiple models, or a structure with multiple copies of the same chain in the asymmetric unit. The example below is for multiple models, with model 1.1 and 2.1 sufficiently similar to be meaningfully superimposed. The three dots ("...") in the two select statements should be filled in such that equivalent atoms are selected. In the example scene below, both structures bind to the same ligand.

	select 1.1 and ...		select 1.1 and ...
Line 40:		Line 40:
	Model 2.1 gets moved and model 1.1 stays in place.		Model 2.1 gets moved and model 1.1 stays in place.

	Here is an example, <scene name='78/786673/Gal_nagal_other_superposition/1'>GAL and NAGAL superimposed via the ligand</scene>. The Jmol script for the scene is here (see Figure X), and the key command is "compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"		Here is an example, <scene name='78/786673/Gal_nagal_other_superposition/1'>GAL and NAGAL superimposed via the ligand</scene>. The Jmol script for the scene is here (see Figure X), and the key command is:

			"compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"

	Use the following buttons to explore the example scene:		Use the following buttons to explore the example scene:


	<jmol>		<jmol>
	<jmolButton>		<jmolButton>

Karsten Theis at 13:16, 31 October 2020

2020-10-31T13:16:24Z

@@ Line 40: / Line 40: @@
 Model 2.1 gets moved and model 1.1 stays in place.
-Here is an example, GAL and NAGAL superimposed via the ligand. The Jmol script for the scene is here (see Figure X), and the key command is:
+Here is an example, <scene name='78/786673/Gal_nagal_other_superposition/1'>GAL and NAGAL superimposed via the ligand</scene>. The Jmol script for the scene is here (see Figure X), and the key command is "compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"
- compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE
 ===Covalent modifications===

Karsten Theis at 13:13, 31 October 2020

2020-10-31T13:13:01Z

← Older revision		Revision as of 13:13, 31 October 2020
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	===Superpositions===		===Superpositions===
			For a superposition, you load a file that contains multiple models, or a structure with multiple copies of the same chain in the asymmetric unit. The example below is for multiple models, with model 1.1 and 2.1 sufficiently similar to be meaningfully superimposed. The three dots ("...") in the two select statements should be filled in such that equivalent atoms are selected. In the example scene below, both structures bind to the same ligand.

			select 1.1 and ...
			show selected
			define set1 selected
			select 2.1 and ...
			show selected
			define set2 selected
			compare {2.1} {1.1} ATOMS{set2}{set1} ROTATE TRANSLATE

			Model 2.1 gets moved and model 1.1 stays in place.

			Here is an example, GAL and NAGAL superimposed via the ligand. The Jmol script for the scene is here (see Figure X), and the key command is:
			compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE

	===Covalent modifications===		===Covalent modifications===

Karsten Theis at 13:00, 31 October 2020

2020-10-31T13:00:05Z

← Older revision		Revision as of 13:00, 31 October 2020
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	wireframe on		wireframe on

	Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase<\scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].		Here is an example, <scene name='78/786673/Gal_overal_view/1'>galactosidase</scene>, and the [http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities Jmol commands used].

	</StructureSection>		</StructureSection>