Michelanglo — Documentation

Details instructions

Raw HTML mode

First, you can only use the code if you have a website that you can edit as raw HTML. Otherwise, you can only share links or zipped html files.

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Not necessarily of the whole page as only a small part is fine. For example:

In the first case, the HTML code is hidden as one sees what one gets as an end result. In the second case, the HTML code is visible: words between tags such as <b> are not styled. In most cases JS can be added here.

If it does not work on your site, it may because some information is lost when you added it.

Try adding to your page:

I am definitely in the correct HTML editor mode as this is <b>enboldened</b> and this is <span id='blue'>blue</span>.<script type="text/javascript">document.getElementById("blue").style.color = "blue";</script><

And view it.

  • If the emboldened text is not bold, but has &gt;b&lt; before it, you were ending your html page in an editor that showed you the end formatting (WYSIWYG) not the raw HTML code.
  • If the emboldened text was bold, but the ought-to-be blue text was not, they the editor may be stripping JS for security reasons or you switched from raw to WYSIWYG before saving and it stripped it.
  • If both displayed as hoped then it is trickier.

On Chrome show the console. To do so press the menu button at the top right next to the your face, then "More tools..." then "Developer tools". Here you can see what went wrong with your page. Is there a "resource not found error"? If so, you may have set it to fetch something that was not there or in that location.

If the demo image gives you an unsolicited black, that means something went wrong with the parsing of the parts. See the else {return 0x000000} //black as the darkest error! line, which is there as a last ditch. To debug this yourself, open the console and type protein.structure.eachAtom(function(atom) {console.log(atom.chainid);}); or in the inner bit atom.resno or other property of atom until you figure out what is wrong with your structure. The variable protein can be obtained with stage.compList[0] if the stage is exposed or if you are using NGL extended script NGL.getStage('viewport').compList[0] or NGL.getStage('viewport').getComponentByType('structure').

If you thing, the fault is in the code please email me. I am aware of two unfixed bugs, one is the CD2 atom in histidine residues with different colored carbons and the other is the absence of shades of gray (_e.g._ `gray40`) in the color chart.

CDN

Add to the bottom of the page, but before the closing of the body element, these two lines:

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<script src="https://unpkg.com/ngl@2.0.0-dev.34/dist/ngl.js" type="text/javascript"></script> <script src="https://www.matteoferla.com/ngl.extended.js" type="text/javascript"></script>

Alternatively, host these two files in your server and link to them.

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<script src="/ngl.js" type="text/javascript"></script> <script src="/ngl.extended.js" type="text/javascript"></script>

These scripts load NGL and allow it to be controlled via data-* attributes of HTML elements (see markup for more)

Viewport

Best option
The recomended way (simple/powerful) is have the viewport declared (in the correct location) like so <div role="NGL" proteins="[{...}]"></div>, where the JSON string value (=in quotes) of proteins is an array of objects like this: {type: 'rcsb|file|data', value: 'PDB id|path|multiline string', loadFx: myOptionalFancyLoadFunction}. Where the optional load function can be added to a script element and can be made from a PyMol file (see PyMol converter).
Full options

There are four inter-compatible ways to declare the viewport.

  • old way. In JS you load it as the NGL suggests, but keeping the stage object globally declared as stage: window.stage = new NGL.Stage( "viewport",{backgroundColor: "white"}); stage.loadFile('static/gfp.pdb') — adding stage as a property of window (i.e.window.stage = …) is the same as declaring without var (i.e.stage = …; cf. var stage = …).
  • Modded old way. As above but you add your stage to the object NGL.stageId thusly var id = "viewport"; NGL.stageIds[id] = new NGL.Stage( id,{backgroundColor: "white"}); NGL.stageIds[id].loadFile('static/gfp.pdb')
  • MultiLoader way. Using the multiLoader function described below (NGL.specialOps.multiLoader('viewport', [{type: 'rcsb', value: '1ubq', loadFx: myFancyLoadFunction}], 'gainsboro')), which allows data-load prolinks to toggle between multiple proteins (pdb strings, custom pdb files or RCSB pdb entries) each with an optional load function.
  • No JS way. Using the attribute role="NGL" on the viewer div-element in combination with prolink data-* attributes, e.g. <div id="viewport" role="NGL" data-load="1ubq" data-focus="residue" data-selection="30:A" data-view="[…]">. If multiple PDB proteins are required, use data-proteins as opposed to load where the value is a comma separated space free list of codes (not array), these can be accessed via data-load=3 prolinks as usual (this is less clear than simply specifying prolinks with data-load with a file or PDB code, but has the sole benefit that, data-load='1ubq' will re-load the file even if 1ubq is loaded, while data-load=2 will not if the current index is 2, however in future unique names will be implemented to avoid this drama). Note that the height issue is sorted and that it can be combined like everything else with click-to-enable-NGL images.
Image

If you are adding an image (as described here), you might need to add it manually as many WYSIWYG editors with insert image buttons (e.g. Blogger) make images that when clicked result in a pop-up with the image fullsize, which is obviously incompatible. Therefore add or edit the image thusly: <div id="viewport"> <img src="my_protein.jpg" alt="my protein" width='100%' style='cursor: pointer'></div>.

The CSS style can be different, but the important thing is that there is a width or a min-width and a height or a min-height —in this example the 0 height is a special case and results in the height being equal to the width.

myData object and multiLoader

The load ability, which uses the add-on NGL.specialOps, works preferably in combination with the add-on NGL.specialOps.multiLoad, which can initialise the scene and handles such things.

The data for load/multiLoader is stored in myData object, which has the property myData.proteins, which is a list of {name: 'unique_name', type: 'rcsb' (default) | 'file' | 'data', value: xxx, 'ext': 'pdb' , loadFx: xxx}. The optional argument loadFx is a function that accepts as argument a NGL protein (component) object and performs requested operations.

The MultiLoader and load can handle img elements in the div, namely the case where you start with an image with labels etc and you click on it and it switches to the viewer.


function nice_ubiquitin (protein) {
        protein.addRepresentation( "line", {color: ..., sele: ...} );
        bla bla
    }
NGL.specialOps.multiLoader('viewport', [{type: 'rcsb', value: '1ubq', loadFx: nice_ubiquitin}], 'aquamarine')
//////////////////////////////id/////////array of elements with loadFx//////////////   ////background
        

The data-load can load proteins from the myData.proteins (and run the custom function LoadFx) if an index is provided.

Prolinks

Links to guide the visitors ('prolinks') are described elsewhere.

Users

By registering the views generated can be retrieved at a latter date.

The sharable links can be viewed by anyone with the link, however, only the registered creator of the page can edit it or promote a registered user who visited the page to edit it.

Admin help

A registered user cannot insert script tags when editing for security reasons. If you require to do so, the site admin can promote your account.

Passwords are hashed, so if forgotten they cannot be retrieved. The site admin can however reset your password.

If you created a page as guest (unregistered user) and somehow lost the PDB or PSE file and want to be able to edit it as a registered user, the site admin can give you edit rights.

If you want to report a page that violates any EU law, the site admin can delete it.

Cookies
  • The password is hashed.
  • Your email is required only if you get in contact regarding an account problem.
  • Your username is visible to the editors of the pages you visit.
  • We will access and edit pages if required to do so.
  • We will not share this information with third parties for whatever reason.

User pages

Once a conversion is done either from a PDB or a PSE, a page is generated.

This page contains several buttons on the right hand side. Most notably "implementation code", which guides the user on how to use the page on their website.

Additionally, the page itself can be downloaded as a self standing page.

Editable

Before downloading the page it may be handy to edit it first. By editing the page, prolinks (protein guiding links) can be made. (see markup documentation for full details)

These user generated pages are accessible by anyone with the URL, but the pages are not listed or can they be cached by search engines. This can be altered in security by ticking encrypt, which will apply AES encryption to it and only who has the encryption key can access it, or conversely, by ticking public it will be listed in Gallery.

NB. The data will not be kept permanently (Storage time TBD).

As a wee present for your reading this documentation, adding ?bootstrap=materials to the url of the pages will switch the framework look to Google Materials. To use this on the download file right click and copy the link and add &bootstrap=materials to it.

  • Snapshot: save png
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If the user is registered, this page can be edited. Do note that a few URL query options are possible: # remote (boolean) boostrap no_user no_buttoons no_analytics