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The Jmol console may be used to obtain information, and to change the scene currently displayed. This may be useful while viewing a Proteopedia page, or while creating a 3D scene, achieving certain effects not possible with the [[Scene Authoring Tools]] alone. You can open the Jmol console via the right-click menu in the Jmol window, or via a dedicated button under the Jmol window in the SAT.
The Jmol console may be used to obtain information, and to change the scene currently displayed. This may be useful while viewing a Proteopedia page, or while creating a 3D scene, achieving certain effects not possible with the [[Scene Authoring Tools]] alone. You can open the Jmol console via the right-click menu in the Jmol window, or via a dedicated button under the Jmol window in the SAT.
<StructureSection load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'>
<StructureSection load='' size='340' side='right' caption='' scene='86/865284/Myoglobin/1'>
==Obtaining information==


<jmol><jmolButton><text>open console</text><script>console</script></jmolButton></jmol><div id=JmolApplet0_console></div>
<jmol><jmolButton><text>open console</text><script>console</script></jmolButton></jmol><div id=JmolApplet0_console></div>
==Obtaining information==


  show sequence
  show sequence
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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>
<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===
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 ...
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, <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"
Use the following buttons to explore the example scene:
<jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme GAL (green) in complex with the sugar galactose. ','white','black');"; javascript @ppdiaCaptionCmd; delay 1.2; model 1</script>
  <text>GAL</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('The enyme NAGAL (blue) in complex with the sugar N-acetyl galactosamin. ','white','black');";
  javascript @ppdiaCaptionCmd;delay 1.5; model 2</script>
  <text>NAGAL</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Superposition of GAL (green) and NAGAL (blue).','white','black');"; javascript @ppdiaCaptionCmd; delay 1.5; model 0</script>
  <text>both</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>animation mode loop; ppdiaCaptionCmd = "changeCaption('Animated superposition of GAL (green) and NAGAL (blue).','white','black');"; javascript @ppdiaCaptionCmd; animation on</script>
  <text>animate</text>
</jmolButton>
</jmol>
===Covalent modifications===
This script shows carbohydrates and the protein side chains that are covalently linked to them as wireframe.
select within(1.8, carbohydrate) and protein
show selected
select within(group, selected)
select selected and (sidechain or alpha)
select selected or carbohydrate
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/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>
</StructureSection>
</StructureSection>

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis
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