# Protein bioinformatics - Lectures & Assignment Q&A - BINF200 H21

This is a shared Q&A document for the lectures and the assignment on protein bioinformatics of BINF200 at the University of Bergen in the autumn 2021. __Please ask questions__ preferrably at the bottom of the document. And add comments and feedback! 😉 You can post anonymously or add your name.

## Links and contact

* [Information at MittUiB](https://mitt.uib.no/courses/29516)
* Lecture 1, 18 Oct
* Proteins and their structure ([PDF](https://mitt.uib.no/courses/29516/files/3401750?wrap=1))
* Protein databases (repetition, [PDF](https://mitt.uib.no/courses/29516/files/3401752?wrap=1))
* Protein structure analysis (until slide 17, [PDF](https://mitt.uib.no/courses/29516/files/3401753?wrap=1))
* Lecture 2, 22 Oct
* Protein structure analysis (from slide 18, [PDF](https://mitt.uib.no/courses/29516/files/3401753?wrap=1))
* Secondary structure inference ([PDF](https://mitt.uib.no/courses/29516/files/3401728?wrap=1))
* Lecture 3, 25 oct
* Tertiary structure inference ([PDF](https://mitt.uib.no/courses/29516/files/3755236?wrap=1))
* 3rd Compulsory Assignment, 29 Oct & 1 Nov
* [Details at MittUiB](https://mitt.uib.no/courses/29516/assignments/51389)
* Files: [.docx](https://mitt.uib.no/courses/29516/files/3770594?wrap=1)/[PDF](https://mitt.uib.no/courses/29516/files/3770593?wrap=1), and _[structure.ipynb](https://mitt.uib.no/courses/29516/files/3770508?wrap=1)_
* Video recording: [Streaming](https://kaf.mitt.uib.no/media/t/0_m4hdktpm/426004), MP4 ([430MB download](https://mitt.uib.no/courses/29516/files/3791165/download))
* **This HackMD document** for shared Q&A, which will be available until "forever". [name=Matus] will keep answering your questions here until the exam, 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 ask by messaging [name=Matus Kalas] on MittUiB or emailing [e-mail]

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## Feedback

**Please** add feedback here, **thanks!** 🙏🏽 With immediate feedback, there is a chance for improvement 😉

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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
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* __FAQ: What is expected in Step 17 of the assignment?__

* The minimum, "compulsory" option is to run this notebook as is, just with your structure. That means you'll only have to change a couple of parameters to fit your structure. However, this is an invitation for you to experiment a bit more on your own. It's very much understood that we're all very busy, so no need to spend __too much time__. 😉 (A pro tip: you can use a "time box" method and give yourself _e.g._ 1 hour ⏳ to play around and see what interesting you get 😊)

__Best source of documentation__, in addition to the example linked above, is the documentation of the original _3Dmol.js_ for JavaScript. The _py3Dmol_ is a wrapper around the [__GLViewer class (see the documentation here)__](http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html), and works in more-or-less exactly the same way (just that the functions return None).

* __Troubleshooting Jalview installation on Mac__
* If your MacOS complaints and doesn't want to run "potentially malicious" Jalview, try the following:

Open "System preferences" on your Mac
Go to "Security & Privacy"
In tab "General" scroll down
Click on "Open anyway" next to where the Jalview app is listed
Done, now should work.

Note: There might be a chance that your whole Mac setup does not allow to do the setup described above. In that case please search the web for a solution how to allow these Security & Privacy / Open anyway settings.

* **I am still unsure as to what you want us to deliver in figure 1.**
* Figure 1 should be the exported image from the multiple sequence alignment and the predictions from it (Steps 6 to 13A).

* **I do not seem to be able to locate the template you showed for figure 5.**
* Figure 5 is only for you to draw a simplified "fold/topology" diagram in 2D, of the secondary and tertiary structure that you predicted. Some examples are in the lecture slides.

* **I wonder if there is a typo in the description for table 6, and that it is possible to combine figure 5 and 6, not 4 and 6 as stated.**
* You can surely combine either 4 & 6 or 5 & 6 into 1 figure if you wish so! 👍🏽 But fair enough, it's not necessarily easy or straighforward to create such combinations. But if you have a creative idea, it will be appreciated!

* **I encounter an Error when trying to execute the alpha fold file (extension ipynb) that I copied on my drive for my protein. I just saved it from google drive as written in the instructions and tried to open it in jupiter notebook; but after running the first cell I see this message: 'ModuleNotFoundError: No module named 'tqdm'' ; and indicated the raw 'import tqdm.notebook'. How can I solve this?**
* Please just create a copy in your Google Drive, but no need to download it to your local computer, as it'd be rather untrivial to run it locally and in Jupyter. Instead, please just execute your copies of the 2 Colab notebooks directly on Google Colab. (And don't forget to double-check that you have GPU selected as accellerator)

* **Which deadline is correct?
Both the pdf and the docx for the assignment have the deadline 18.11, while MittUiB has 14.11**
* Oh no, sorry for the confussion! 😦 Indeed the docx/PDF says 14 Nov on the top, and 18 Nov on the bottom with the list of deliverables. Sorry for that 🙁 Anyhow, million thanks all for submitting on time, and you now have until the 18th midnight to do eventual improvements if you want to.

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