Jmol/Surfaces: Difference between revisions
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== Examples and Jmol commands to modify them == | == Examples and Jmol commands to modify them == | ||
Here is the surface of <scene name='87/871286/Rnase_a/2'>RNAse</scene>. It is shown with the default parameters "frontlit" and "frontonly". | === Plan vanilla overall surface === | ||
Here is the surface of <scene name='87/871286/Rnase_a/2'>RNAse</scene>. It was created with the [[Scene Authoring Tools]], and it is shown with the default parameters "frontlit" and "frontonly". | |||
You can decide whether to show or hide the surface occluded by other parts of the surface: | You can decide whether to show or hide the surface occluded by other parts of the surface: | ||
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</jmolCheckbox> | </jmolCheckbox> | ||
</jmol> | </jmol> | ||
=== Slabbing surfaces === | |||
Surface can get busy easily. One way to make the scene easier to understand is to cut away the parts of the surface that are less important for the point you are trying to get across. Here are two examples of slabbing: | |||
<jmol> | |||
<jmolRadioGroup> | |||
<item> | |||
<script>isosurface ID "1" slab none</script> | |||
<text>intact</text> | |||
<checked>true</checked> | |||
</item> | |||
<item> | |||
<script>isosurface ID "1" slab none; isosurface ID "1" slab within 12.0 {@44} | |||
</script> | |||
<text>clipped by 12 A sphere</text> | |||
<checked>false</checked> | |||
</item> | |||
<item> | |||
<script>isosurface ID "1" slab none; isosurface ID "1" slab -(atomno=343) (atomno=858) (atomno=587) | |||
</script> | |||
<text>on one side of plane</text> | |||
<checked>false</checked> | |||
</item> | |||
</jmolRadioGroup> | |||
</jmol> | |||
You can try these for a solid or a transparent surface: | |||
<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenUnChecked>isosurface ID "1" transparent 0 | |||
</scriptWhenUnChecked> | |||
<scriptWhenchecked>isosurface ID "1" transparent 60 | |||
</scriptWhenchecked> | |||
<checked>true</checked> | |||
<text>transparent</text> | |||
</jmolCheckbox> | |||
</jmol> | |||
</StructureSection> | </StructureSection> | ||
