User:Eric Martz/Sandbox 17

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This page created 2020/12/16 after Jaim made changes to enable caption editing.
This page created 2020/12/16 after Jaim made changes to enable caption editing.
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<br>1. <scene name='87/870563/Pngj_with_caption_2020-12-16/1'>Here is a new PNGJ scene with a caption</scene>.
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<br>1. <scene name='87/870563/Pngj_with_caption_2020-12-16/1'>Here is a new PNGJ scene with a caption</scene>. This loads '''Image:6zgi-cavities.pngj'''
<br>When scene 1 was re-loaded, the caption DID APPEAR for editing, but in JSmol, the isosurfaces from the PNGJ file were not displayed.
<br>When scene 1 was re-loaded, the caption DID APPEAR for editing, but in JSmol, the isosurfaces from the PNGJ file were not displayed.
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<br>2. <scene name='87/870563/Pngj_with_caption_2020-12-16/2'>Here I have re-loaded scene 1, edited the caption, and saved</scene>.
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<br>2. <scene name='87/870563/Pngj_with_caption_2020-12-16/2'>Here I have re-loaded scene 1, edited ONLY the caption, and saved</scene>.
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<br>As in the SAT, the isosurfaces in the PNGJ file have disappeared.
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<br>As in the SAT, the isosurfaces in the PNGJ file have disappeared. But the edited caption appears correctly.
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----
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2020-12-17:
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<br>3. <scene name='87/870563/Pngj_with_caption_2020-12-16/3'>Scene 1 saved after editing only the CAPTION</scene>, after further fixes by Jaim (2020-12-17).
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<br>BOTH SCENE AND CAPTION ARE CORRECT. HURRAY!
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Scenes 4 and 5 use '''Image:6zgi-membrane-proximal-cavity-jmol-cr2.5.pngj'''.
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<br>4. <scene name='87/870563/6zgi_mem-prox_cav_4_colors/1'>New PNGJ with membrane-proximal cavity in 4 colors</scene>. These isosurfaces take several minutes to calculate, but when saved as JVXL files, then loaded from the files and cached, and that saved into a new PNGJ file, the results appear in about one second!
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----
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2020-12-19:
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<br>5. This green link runs a JSmol script, loading the PNGJ file, and writing the caption directly.
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<jmol>
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<jmolLink>
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<script>
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set echo false;set echo middle center; echo "Loading Model";color echo red;delay 0.1;
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load "http://proteopedia.org/wiki/images/3/3d/6zgi-membrane-proximal-cavity-jmol-cr2.5.pngj";
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spin on;
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capcmd = "changeCaption(`Four isosurfaces in 4 colors from [[6zgi]].`, '', '')"
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javascript @capcmd
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</script>
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<text>Membrane-proximal cavity in SARS-CoV-2 spike protein.</text>
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</jmolLink>
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</jmol>
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I have not been able to devise a method to color text in the caption. Anything with &lt; or &gt; creates an XML error (page cannot be saved). Using e.g. &amp;lt; can be saved, but confuses JSmol which expects a new command after the ';'.
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Proteopedia's wiki lacks Template:Font_color: {{font color|red|red text?}}.
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6. I tried an indirect method to color caption text. This page saves in Proteopedia, and the JSmol variable captext prints correctly. I can't tell if my assignment to the Javascript variable captext is working. The caption does not display. There are no JSmol errors. There are Javascript warnings, but not errors.
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<jmol>
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<jmolLink>
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<script>
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script "http://proteopedia.org/wiki/images/6/69/Colortext.spt"
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# captext JSmol variable is only for testing.
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captext = "Words with " + colortext("some red", "red") + " in this caption."
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javascript captext = "Words with " + colortext("some red", "red") + " in this caption."
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capcmd = "changeCaption(captext, '', '')"
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javascript @capcmd
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</script>
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<text>Colored caption test.</text>
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</jmolLink>
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</jmol>
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----
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2020-12-21:
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7. <scene name='87/870563/2020_12_21_retry_4_isosurfaces/1'>Re-try of the 4-isosurface PNGJ</scene> (Image:6zgi-membrane-proximal-cavity-jmol-cr2.5.pngj). WORKS.
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8. <scene name='87/870563/2020_12_21_retry_4_isosurfaces/2'>Same scene as 7 with caption edited to include colored text</scene>. WORKS WITH COLORED CAPTION. COLORS done with span classes.
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9. <scene name='87/870563/2020_12_21_retry_4_isosurfaces/3'>Same as 8 but with yellow caption text done as a style span</scene>. DOES NOT WORK.
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10. <scene name='87/870563/2020_12_21_retry_4_isosurfaces/4'>Same as 9 but with non-breaking space codes removed</scene>. STILL DOES NOT WORK. Evidently style spans are not supported in captions.
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11. <scene name='87/870563/2020_12_21_retry_4_isosurfaces/5'>Yellow background text changed to a class span</scene>. WORKS.
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====PDB (not PNGJ) scenes====
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12. <scene name='87/870563/No_isosurfaces_1d66/2'>A simple scene (no isosurfaces) for testing caption text coloring</scene>. WORKS. FONT COLOR TAGS CAN BE USED IN SCENES NOT INVOLVING PNGJ FILES, BUT BE SURE TO DO BOLD/ITALICS WITH HTML TAGS NOT WIKI MARKUP!
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13: <scene name='87/870563/No_isosurfaces_1d66/3'>Test using a color scheme template</scene> for Oxygen. FAILS.
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14: <scene name='87/870563/No_isosurfaces_1d66/4'>Single color template method</scene>: <nowiki>{{Font color|red|red text}}</nowiki>. DOES NOT WORK.
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15: <scene name='87/870563/No_isosurfaces_1d66/5'>Span style method</scene>. FAILS PREVENTING SCENE OR CAPTION FROM LOADING AT ALL.
</StructureSection>
</StructureSection>
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==See Also==
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* [[Image:Colortext.spt]]
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* [[Proteopedia:DIY:Templates]]

Current revision

PNGJ scene and caption tests

Drag the structure with the mouse to rotate

See Also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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