Jmol/State: Difference between revisions
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== Retrieving a compact portable script == | == Retrieving a compact portable script == | ||
In some situations, the state script is not as valuable as the Jmol commands entered to create the scene. If you want to make a similar scene with different coordinates or want to use the script for training purposes, a compact, portable, human-readable script rendering the same scene as the state script is desirable. | |||
The | The state script relies on the exact order of atoms (and exact order of generated bonds) in the file. If you inadvertently apply the state to coordinates slightly different from the original, the resultant scene might look corrupted (i.e. it does not make sense). In this context, the state script is less portable than the Jmol commands used to generate it. It is also typically less compact and less readable for humans. While the history of issued commands is often not available directly, it is possible to reverse-engineer a compact set of commands that is portable to different coordinates, or can serve as an example to make a similar scene. | ||
Another challenge are commands that get expanded (made explicit) in the state script. | The main challenge in retrieving a compact list of commands are the atom and bond selections. For example, to draw all arginine side chains in a space-filling mode, you could issue the Jmol commands "select arg and sidechain; spacefill on". In the state script, this will show as two selection commands and two spacefill commands. The first selection is a list of atom numbers corresponding to the carbons of the arginine side chain, and the second a list of the nitrogens (because they are shown by default with different radii). For a trained human, it is fairly easy to reverse-engineer the selection by displaying the selected atoms, and by using commands such as "show sequence", "show selected" and "show coordinates". | ||
Another challenge are commands that get expanded (made explicit) in the state script. The "spacefill" command with default atomic radii mentioned above is one example. Another example is applying a rainbow or CPK color scheme. In the state script, every single color will be represented by a distinct set of commands. However, if you are familiar with the color schemes, it should be straightforward (but tedious) to get a compact command that reproduces the scene. | |||
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. | ||
