# Compulsory Assignment 3 - BINF200 H20

This is a shared Q&A document for the work on the Compulsory Assignment 3 of BINF200 at the University of Bergen in the autumn 2020. __Ask questions at the bottom__ of the document. You can ask anonymously or add your name.

## Links and contact

* [Information at MittUiB](https://mitt.uib.no/courses/23753/discussion_topics/200303)
* Assignment instructions (in [PDF](https://mitt.uib.no/courses/23753/files/2891071/download?wrap=1) or [DOCX](https://mitt.uib.no/courses/23753/files/2891072/download?wrap=1))
* Jupyter Notebook ([structure.ipynb](https://mitt.uib.no/courses/23753/files/2891073/download?wrap=1)) for visualisation
* You are welcome to use one of the computer rooms in Realfagbygget, especially if you do not have good working conditions at home, or need a bigger screen or a desktop computer. We will have the interactive help sessions physically in [1003](http://use.mazemap.com/?v=1&campuses=uib&sharepoitype=identifier&sharepoi=308:1B6D); while [1001](http://use.mazemap.com/?v=1&campuses=uib&sharepoitype=identifier&sharepoi=308:1C7A) and [1002](http://use.mazemap.com/?v=1&campuses=uib&sharepoitype=identifier&sharepoi=308:1B7A) are empty most of the time, so feel free to use them. [1003 availability here.](https://tp.uio.no/uib/timeplan/?type=room&building%5B%5D=308&id%5B%5D=3081B6D) Of course as long as you're not quarantined or isolated :(
* Interactive sessions on Zoom, Wed 4 Nov 08:30-12:00 and Thu 5 Nov 08:30-10:00, where you can work on the assignment and get immediate answers to your questions (using Zoom breakout rooms and chat).
* [Recorded video introduction](https://drive.google.com/file/d/1LWt8ESAHw_iN9S8nwybDcTXGm9CSVv1Y/view?usp=sharing), mostly to Jupyter Notebook and Lab (stream or download MP4 150MB).
* This HackMD document for shared Q&A, which will be available until "forever". [name=Matus] will keep answering your questions here, and feel free to "+1" others' questions or answer them yourself if you have a good answer.
* If you want to ask privately, you can do it during the Zoom sessions (in your breakout room or private chat), or anytime afterwards by messaging [name=Matus Kalas] on MittUiB or emailing [e-mail]

## How to edit in HackMD

If you see this page in **view mode**, what you probably do after opening it, click on *Edit* on the top. Later you can always do either of the following to enable editing:
1. **Edit mode**: Ctrl+Alt+E, or click the button with a pencil on the top left to switch to edit mode
2. **Both mode**: Ctrl+Alt+B, or click the button with a square with a vertical line in the middle (among the 3 buttons on the top left). Nice with a big-enough screen.

## Feedback

Add any feedback here, for immediate or next-time improvements.

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## Questions and answers

Please **ask new questions at the bottom** of this document. You can ask anonymously, or write your name.

* writing e.g. `[name=Lisa]` will show up as [name=Lisa]

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* A sample question: How to write a question using **markdown** in HackMD?
* You can just add a new line or a couple, and you can add a bullet point (`*`), use **bold** or *italics*, [links](https://mitt.uib.no), etc.
* You can nest and indent bullet points under each other like this (using tab or at least 2 spaces)

* [name=Matus] Another question: What to ask first?
* ...
* ..
* blahblah
*

* [name=Matus] There have been a couple of **common technical problems with Jupyter** during the interactive session. Listing solutions here:
* Note: The following points are now mentioned also in the **updated** *[structure.ipynb](https://mitt.uib.no/courses/23753/files/2891073/download?wrap=1)* or *[Compulsory Assignment 3.docx](https://mitt.uib.no/courses/23753/files/2891072/download?wrap=1)/[pdf](https://mitt.uib.no/courses/23753/files/2891071/download?wrap=1)*
* Some of your **Anaconda/Miniconda** installations don't have conda channels set up in a standard way. No worry. This way the `py3Dmol` installation will work for all of you with (Ana/Mini)conda:
`conda install -c conda-forge py3Dmol`
* It doesn't matter if you use **Jupyter Notebook or Jupyter Lab** in the assignment. Jupyter Lab is just Jupyter Notebook with an additional "IDE" (integrated development environment) around it. Choose the one you like more or the one that works better on your computer.
* Note: Installing the extension
`jupyter labextension install jupyterlab_3dmol`
is only needed in you want to use Jupyter Lab
* To execute a "cell with code" (box) inside a Notebook, click anywhere inside this cell, and press **Ctrl+Enter** or **Cmd+Enter**
* On some MacOS setups you need Ctrl+Enter, and on some Cmd+Enter to execute the cell
* **Something what is easy to forget when working fast:** If you change something in the code and want to re-run it to get a new output, you also have to re-run the subsequent cells that depend on it, and sometimes also preceding cells that this cell depends on. _(Notebook works like any other Python interpreter. But it's always just one cell (snippet of code) that is executed at a time.)_
* For this assignment, use the **structure.ipynb** notebook. [Download it from MittUiB](https://mitt.uib.no/courses/23753/files/2891073/download?wrap=1) and open it in Jupyter by finding it in your folders (inside Jupyter) and clicking on it. Please make sure it's **saved** after you make changes and/or run it. Sometimes it saves automatically, but sometimes it doesn't :(

* [name=Matus] The minimal **3D visualisation** requirement for this assignment is to *re-run* the provided _structure.ipynb_ notebook with your model from SWISS-MODEL. However, you are encouraged to do a bit more experimenting and coding with py3Dmol to create an even cooler visualisation.

* If you want [copied from the **updated** version of *[Compulsory Assignment 3.docx](https://mitt.uib.no/courses/23753/files/2891072/download?wrap=1)/[pdf](https://mitt.uib.no/courses/23753/files/2891071/download?wrap=1)*], an excellent option is to download your *model01.pdb* file from SWISS-MODEL (click Model 01 > PDB Format), and open it in Jalview together with your alignment and secondary structure predictions. *E.g.* in your “JPred Secondary Structure Prediction **for** visible…” windows, right-click / 2-finger-click on the name (ID) of **your unknown sequence** on the left > 3D Structure Data > dropdown From File > Select PDB File > New View. This will allow you to **compare your predicted secondary structure and disorder with your predicted tertiary structure**. Hovering with your mouse/touchpad cursor over a residue in the sequence will also show the residue in the 3D structure, and vice versa, helping you to compare the predictions (a bit clumsy but very useful, use patience with the hovering). Note: For that, you need to see both the alignment/JPred window and the 3D structure Jmol window at the same time inside Jalview. Extra cool: The colouring of your sequence is visible in the 3D structure, so why not trying with colouring of Hydrophobicity, secondary structure elements (Colour > By Annotation > jnetpred), and/or Protein Disorder? You can check out this video for some more info: [3D Molecular Structure Jmol and UCSF Chimera viewers in Jalview](https://www.youtube.com/watch?v=yRBLIukwdH4&feature=youtu.be) (5min).

* [name=Matus] The optional _de novo_ coevolution-based structure prediction with [EVcouplings](https://) seems to take many days (possibly depending on the chosen parameters). So if you want to try it, supply your email address when submitting the job to get notifications, and be ready to wait for days ;-)

* 👩🏻‍💻️👩🏽‍💻