Merge pull request #3 from jmbuhr/self-contained

Self contained

README.md

@@ -24,14 +24,20 @@ Likewise, the example rendered as a revealjs presentation (`presentation.qmd`) i
 
 ## Limitations
 
-- No self-contained htmls: Molstar viewers for local files are empty when the file is **not** served by a webserver such as `quarto preview` or GitHub pages.
-This means it will not display your molecule when you simply open the rendered html with a browser,
-even if you set the html to be self-contained.
-The reason for this is the [Same-origin Policy](https://developer.mozilla.org/en-US/docs/Glossary/Same-origin_policy), a security measure in web browsers.
-It and similar policies prevent that one document can access resources it is not supposed to access.
-For example, an html document you downloaded is not allowed to execute code that reads personal files on your computer.
-This also prevents it from loading your molecules from local paths.
-- revealjs presentations now use iframes instead of a normal div to work around https://github.com/jmbuhr/quarto-molstar/issues/1, which is why you might have to address those differently for custom styling if you plan to use the same source for html and reveal output.
+- Self-contained htmls:
+  Molstar viewers for local files are empty when the file is **not** served by a webserver such as `quarto preview` or GitHub pages.
+  This means it will not display your molecule when you simply open the rendered html with a browser,
+  even if you set the html to be self-contained.
+  The reason for this is the [Same-origin Policy](https://developer.mozilla.org/en-US/docs/Glossary/Same-origin_policy), a security measure in web browsers.
+  It and similar policies prevent that one document can access resources it is not supposed to access.
+  For example, an html document you downloaded is not allowed to execute code that reads personal files on your computer.
+  This also prevents it from loading your molecules from local paths.
+
+  For plain text formats in the `mol-url` shortcode, such as `pdb` and `xyz`, you can enable a custom option that circumvents this limitation 
+  by embedding them straight into the html as a string.
+  Add `molstar: embed` to your yml frontmatter to use this.
+- revealjs presentations now use iframes instead of a normal div to work around https://github.com/jmbuhr/quarto-molstar/issues/1,
+  which is why you might have to address those differently for custom styling if you plan to use the same source for html and revealjs output.
 
 ## Update Mol* (extension developement)
 

_extensions/molstar/assets/app-container.css

@@ -5,3 +5,6 @@ div .molstar-app {
   margin-bottom: 1rem;
 }
 
+.msp-plugin .msp-layout-expanded {
+    z-index: 1;
+}