Jmol/State: Difference between revisions
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Proteopedia uses the Jmol<ref>DOI: 10.1107/S0021889810030256</ref> viewer to show molecules in three dimensions. What Jmol shows is described by its [[Jmol/State|state]]. The state is a set of Jmol instructions, available for viewing in the Jmol console and for saving as state script or as part of a so-called PNGJ file. Executing the state script is a way of recreating a scene previously saved. | Proteopedia uses the [[Jmol]]<ref>DOI: 10.1107/S0021889810030256</ref> viewer to show molecules in three dimensions. What Jmol shows is described by its [[Jmol/State|state]]. The state is a set of Jmol instructions, available for viewing in the Jmol console and for saving as state script or as part of a so-called PNGJ file. Executing the state script is a way of recreating a scene previously saved. | ||
== Parts of the State == | == Parts of the State == | ||
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The coordinates are loaded in _setFileState, and drawing commands are issued in _setModelState. Commands issued in the other four sections will also affect what is displayed. Parts of the scene might be hidden by commands in _setSelectionState. The exact appearance of the scene is dependent on parameters set in _setWindowState and _setParameterState, and the initial view (orientation, size, centering) is dependent on commands in _setModelState. | The coordinates are loaded in _setFileState, and drawing commands are issued in _setModelState. Commands issued in the other four sections will also affect what is displayed. Parts of the scene might be hidden by commands in _setSelectionState. The exact appearance of the scene is dependent on parameters set in _setWindowState and _setParameterState, and the initial view (orientation, size, centering) is dependent on commands in _setModelState. | ||
In Proteopedia, some parts of the Jmol state are changed after saving from the [Scene | In Proteopedia, some parts of the Jmol state are changed after saving from the [[Scene Authoring Tools]] to allow loading of locally saved coordinates and enable features such as the scene caption and transitions from the previous scene. | ||
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Finally, some atom selections are based on distance criteria or properties (e.g. secondary structure) that are not obvious from the output of a "show selected" command. Often, these types of selections start making sense in the context of the scene, the figure caption and the accompanying text. If they don't make sense, you can still "translate" the list of atom numbers into a list of residue numbers and atom types, improving readability and portability. | Finally, some atom selections are based on distance criteria or properties (e.g. secondary structure) that are not obvious from the output of a "show selected" command. Often, these types of selections start making sense in the context of the scene, the figure caption and the accompanying text. If they don't make sense, you can still "translate" the list of atom numbers into a list of residue numbers and atom types, improving readability and portability. | ||
Here is [https://youtu.be/3G4CjIzSR3c an example] of figuring out a short script that describes an existing scene. | ==Example Explained on YouTube== | ||
Here is [https://youtu.be/3G4CjIzSR3c an example] of figuring out a short script that describes an [[Talk:Hen_Egg-White_%28HEW%29_Lysozyme|existing scene]]. | |||
==See Also== | |||
* [[Jmol/Index]], a list of Jmol-related resources. | |||
== References == | == References == | ||
<references/> | <references/> | ||
