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A script to transpile a PyMOL PSE file to a NGL view
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README.md

Michelaɴɢʟo

Michelaɴɢʟo is a web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site.

Click here to visit the web app (temp URL).

For the documentation for the web app see help page.

Non-Michelaɴɢʟo goodies

The conversion file, michelanglo/transpiler.py and the files in michelanglo/transpiler_templates are all that is required to use locally. They are in michelanglo_app to avoid allowing the app to do a relative import beyond the top-level package (michelanglo_app).

The js that allows web content creators to control NGL without using JS is michelanglo_app/static/ngl.extended.js, while its documentation is at ngl.matteoferla.com/markup.

Aim of Michelaɴɢʟo

The aim of this app is to provide a way for a user to easily generate a web-ready output that can be pasted into a webpage editor resulting in an iteractive protein view.

Therefore the intended audience are biochemists that may not have any web knowledge that wish to display on their academic pages their researched protein.

A future possibility is that in collaboration with specific journals this could be rolled out in papers.

process

Script

The following describes the script. For the documentation for the web app, such as forgotten passwords, cookie usage etc., see help page.

Transpiler

The script, and associated web app, gets a PSE file and converts it to a copy-pastable piece of code.

If needed, this piece of code can include the PDB data itself, thus removing the need to store the PDB file somewhere.

Image

Whereas, the most commonly used protein viewing software is PyMol, most researchers render a view and label/draw upon it in Paint/Powerpoint/Photoshop.

Consequently, the code allows users to generate code than when a given static image is clicked it results in a NGL viewer div. Example: demo.

The mouse image can be found here.

Script functionality

The script PyMOL_to_NGL.py has the class PyMolTranspiler. Which accepts different starting values. If Pymol is installed on the system and the system is not a Windows machine, the filename of the PSE is passed and processed.

which can be initialised thusly:

>>> trans = PyMolTranspiler(view=get_view_output_as_string, reps=interate_output_as_string, pdb=file_of_saved_pdb)
>>> trans.to_html_line()

    <!-- **inserted code**  -->
    <script src="https://cdn.rawgit.com/arose/ngl/v0.10.4-1/dist/ngl.js" type="text/javascript"></script>
    <script type="text/javascript">
                var stage = new NGL.Stage( "viewport",{backgroundColor: "white"});
                stage.loadFile( "rcsb://1UBQ").then(function (protein) {
                    window.protein=protein;
                    var m4 = (new NGL.Matrix4).fromArray([0.7028832919662867, -15.555627368224188, -42.22285806091866, 0.0, 44.899153041969875, 3.027791553007612, -0.36819969318162726, 0.0, 2.968061030936039, -42.12016318698766, 15.567270234463177, 0.0, -26.235111237, -28.054784775, -3.878722429, 1.0]);
                    stage.viewerControls.orient(m4);
                    protein.removeAllRepresentations();
                    var sticks = new NGL.Selection( "1.N or 1.CA or 1.C or 1.O or 1.CB or 1.CG or 1.SD or 1.CE or 30.N or 30.CA or 30.C or 30.O or 30.CB or 30.CG1 or 30.CG2 or 30.CD1" );
                    protein.addRepresentation( "licorice", { sele: sticks.string} );
                    var cartoon = new NGL.Selection( "14 or 15 or 19 or 1 or 13 or 16 or 11 or 17 or 12 or 20 or 18 or 10 or 2" );
                    protein.addRepresentation( "cartoon", { sele: cartoon.string} );
                    stage.viewerControls.orient(m4);
                });
    </script>
    <!-- **end of code** -->

The The class initialises as a blank object with default settings unless the file (filename of PSE file) or view and/or reps is passed. For views see .convert_view(view_string), which processes the output of PyMOL command set_view For representation see .convert_reps(reps_string), which process the output of PyMOL command iterate 1UBQ, print resi, resn,name,ID,reps

The source of the NGL code can be changed:

>>> trans.to_html_line(ngl='ngl.js')

Example

Here is a rather funny view in PyMOL and the equivalent snapshot transpiled to NGL (link to example.html).

Where

The script output a secret temporary page that can be shared, but also a block of code that can be used by the user on their sites.
About the latter usage, to use the output code one needs access to the raw HTML. 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.

data-toggle='protein'

Extra functionality can be optionally added, including the ability to create links that control the protein.

The full documentation and examples can be found at ngl.matteoferla.com/markup.

Briefly, <a href='#viewport'>you see this text as a link</a> is technically called an anchor element and is commonly called a link. Like all HTML elements, everything with the within the lesser-than and greater-than symbols controls its behaviour. The href attribute () tells the browser where to point, either to another page or to an element within the page —the hash symbol means the elements id attribute, its unique name. Following JQuery and Bootstrap behaviour, if a data-toggle='protein' is added the code will know to change the protein depending on the other tags. If a data-residue='23' is added a residue index and it's neighourhood is focused on (for chains, use a synthax like 23:A), for a region use data-region='23-45'. Optionally, data-title controls the text that appears in the viewer, while data-color (US spelling) controls the colour of the selection. The default values for the latter are green for regions and hotpink for residues —See here for HTML colour names, for a specific PyMOL colour RGB value, follow the commands in this PyMOL Wiki page and then convert it to a hex code.

Issues

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 you thing, the fault is in the code please email me.

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? That 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 atom.resno or other property of atom until you figure out what is wrong with your structure. 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.

Technicalities

Parts to convert

Three parts are needed to convert a .pse file into a NGL view.

  • the model
  • orientation
  • representation
    • lines, sticks, cartoon etc.
    • colors
    • surface (handled differently in NGL)

Additionally, there are

  • text/labels which are normally added in photoshop by people...
  • arrows, which are great, but in PyMol are from the add-on script cgo_arrows and not part of the native code

Notes on PSE side

A Pse is encoded, so there is no way to read it except with Pymol. But Pymol can reveal it's secrets.

Orientation

I was driven spare with converting the orientation. It simply was a question of inverting the sign on the $\vec{x}$ and $\vec{z}$ of the rotational matrix, multiplying it by the absolute of the scale and adding the origin of rotation's position with inverted sign. For more see my notes on the conversion of the view

Representation

The atom information is kept in reps. Say PyMOL>iterate 1UBQ, print resi, resn,name,ID,reps. This is an integer with no information give. However, looking at how it behaves it is clear it is a binary number where each position controls lines, sticks, cartoon and surface.

  1. Sticks
  2. Spheres
  3. Surface
  4. Label (needs additional variable)
  5. Non-bounded spheres
  6. Cartoon
    • putty is a special cartoon rapresentation: iterate sele, resi,name,reps,cartoon
  7. Ribbon
  8. Lines
  9. Mesh
  10. Dots
  11. Non-bounded —Ligand (HETATM) properties are otherwise the same
  12. Cell

Primitive equivalence table

PyMol PyMol reps bit NGL
spheres 000000000010 spacefill
NA ball+stick
NA helixorient
lines 000010000000 line
sticks 000000000001 licorice
NA hyperball
NA trace
ribbon 000001000000 backbone
NA ribbon
cartoon 000000100000 cartoon
surface 000000000100 surface
label 000000001000 label
non-bounded spheres 000000010000
NA rope
"putty"* tube
mesh 000100000000
dots 001000000000 point
non-bounded 010000000000
cell 100000000000 cell

∗) The two differ in how this is handled.

The SS problem

NGL does not assign secondary structure. Therefore, if not specified everything will be a turn/loop, so both the helices and sheet (especially) will look anemic.

The script SS.py can generate this in PDB file via PyMol. However, the generated SHEET definition is not as it ought to be, as it gives out mulitple separate strands as opposed to a single multistrand sheet —It works though, so who cares?

Complicated?

The code seems a bit complex when it comes to selections. The most obvious thing to do is to just have a list of the atoms with a given color and representation. However, this has two problems: first, the NGL atom serial does not always map to the same PyMOL atom ID as both try to fix issues in PDB atom id, the second is that having a list of thousands of ids quickly becomes heavy.

Python3 compiled Pymol in Ubuntu

This app requires Python3 compiled Pymol. The best option is using Conda. Otherwise it needs to be compiled (instructions).

Webapp installation

Additionally for the webapp the package needs to be installed and the database started.

#use whatever venv or system pip/alembic you want.
pip3 install -e .
alembic -c production.ini revision --autogenerate -m "lets get this party started"
alembic -c production.ini upgrade head

In windows the excecutables will have .exe suffixes and are in Scripts folder C:\Users\matteo\AppData\Local\Continuum\anaconda3\Scripts\pip3.exe say for your regular install, your virtual env will be wherever you put it.

Afterwhich, change the secret in production.ini and run the script and made a user called admin. The users trashcan gets generated automatically when a guest makes a view and is blacklisted along with guest and Anonymous.

Licence

  • PyMOL is a trademark of Schrodinger, LLC, and can be used freely.
  • NGL uses an MIT licence.
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