View source for Jmol/Using the console

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'>
==Obtaining information==

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

 show sequence

This shows the residues that contain selected atoms

 show selected

This shows which atoms are selected

 show coordinates

This shows the coordinates of selected atoms

 show measurements

This shows all the distances and angles that are displayed

==Changing the scene==

===Surfaces===

===Electron density===

===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, <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:


<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

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>