media:jymol_examples
JyMOL Examples
These examples can be run using the “make -f Makefile.demo DEMO_NAME=<demo-name>” command from the JyMOL distribution.
For example, to run the first demo, you can type in:
make -f Makefile.demo DEMO_NAME=align.Align
Note: You will also need to make sure the JAVA_HOME variable is set properly.
| Example | Description |
|---|---|
| align.Align | loads in proteins, aligns a couple of them together, and prints the outputs of align. |
| cardbug.CardBug | sets up a combobox with two settings that change JyMol's view when changed. |
| cgo.CGO | creates a CGO, sets it with different types of objects, and loads it into JyMOL. |
| figure.Figure | Shows two buttons off to the right that calls ray() and draw(). resulting images are shown in a separate window. |
| gpcr.GPCR | Load a PDB, and show protein in yellow and ligand as sticks |
| isomesh.Isomesh | Load a PDB, an XPLOR map file, and generate an isomesh |
| isosurface.Isosurface | Load a PDB, an XPLOR map file, and generate an isosurface |
| jardata.JarData | reads an input protein directly from a Jar file and loads it into JyMOL. |
| jymolign.JyMolign | Interface with GUI widgets to show how control objects and do simple commands with JyMOL. |
| measure.Measure | Load in example molecule and add/get measurements distances, angles, dihedrals, and change parameters for visual elements. |
| misc.Misc | Load in example molecule and label carbons. |
| pseudoatom.Pseudoatom | Load in a small molecule and add some atoms using pseudoatom in a couple of ways. Also, hooks up a ClickConsumer to show how to capture a click event with picking information. |
| select.Select | Loads a small molecule and selects 3 atoms using selectList(). |
| setting.Setting | Goes through different settings and shows the results as the user presses a key. |
| simple.Simple | Loads a simple molecule and shows the surface. |
| views.Views | Shows how to get and change the view calling getView() and setView() |
media/jymol_examples.txt · Last modified: 2013/08/19 21:00 (external edit)
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