How to use PyMOL free libre, or | How to compile PyMOL from source on Ubuntu 18.04

This will allow you to run PyMOL without an aqcuired license which you certainly would need if you were to use the compiled binaries provided from the PyMOL website. This is just a very simple guide providing a list of the packages you need to install, and showing how to run the scripts you need to download the source code and compile the program.
The version of the program will be a little stripped of menus and such, so you will need to rely more on command line interface arguments to use it.

From what I can gather the program used to be totally free, but the original developer passed away unexpectedly in 2009, after which it was acquired by Schrödinger, Inc. While the company does keep some of their updates closed source, requiring users to pay for a license, most of the functionality is still there in the Open Source version. There are also some rumors of provided binaries out there, but if you compile it yourself like this here, you will be sure to have the latest updates (last update 21 days ago at the time of writing), and you don't have to trust a third party not to put a virus in the program they give you for free for no reason.

If you're interested to see when the project was last updated, or just inspect the code, visit the project on github:
https://github.com/schrodinger/pymol-open-source

Now, just run these commands in your terminal and you should end up with a pymol executable on your computer in just a few minutes!

Install the required dependencies for compiling:

sudo apt-get install freeglut3-dev libglew-dev mesa-utils mesa-common-dev binutils libxml2-dev libmsgpack-dev python3-pip libglm-dev libpng-dev libfreetype6-dev git

Install the python Qt5 library, which is a python library, so it has to be installed with the python package manager pip that you just installed:

pip3 install PyQt5

Download the source code (i.e. clone the git repository)

git clone https://github.com/schrodinger/pymol-open-source.git

Enter the pymol source code directory that was just downloaded by git:

cd pymol-open-source

Run the install script, placing the compiled binaries in $HOME/programs/PyMOL or wherever you like

python setup.py install --prefix=~/programs/PyMOL/ --use-msgpackc=no

(Optional) Add the location of the compiled executable to your PATH, so you can run the program from anywhere in the terminal:

put the following in ~/.bashrc

export PYMOL_HOME=$HOME/programs/PyMOL
export PATH=$PATH:$PYMOL_HOME/bin

Now close your terminal and open a new one to reload the PATH variables.

And finally run

pymol

Or, if you didn't do the optional PATH step, cd into the directory you specified when running the script, and run ./pymol

You can also make a menu short cut entry by copying one of the .desktop files in /usr/share/applications/ and changing it to point to the location of your pymol executable.

How Bioinformatics is supporting medicine and drug development

This post is more of an article type which is supposed to distill and simplify, and present some basic information on how the field of bioinformatics supports medicinal drug development and other biological research. For me it is a very interesting field as I am formally educated in both Computer Science and Molecular Biology and Biochemistry. Having deep fundamental understandings of both fields (although of course I could understand it even better) really makes it practical when you for instance need to compile or modify the source code of a program, when all you really wanna do is play around with a 3D model of a protein.

I noticed this first hand today while I was writing this article and I wanted to include some graphics made in PyMOL, and I realized that since I'm not a student anymore, I can't use the educational license given to me by the University for the binaries that the PyMOL guys provide, however, if you compile the PyMOL open source project from source yourself, you don't need a license! So great. I mean, compiling anything from source at all isn't really that difficult if all the dependencies are in a readily available repository, but I think most people wouldn't even think to look in their respective readily available repositories because sometimes you need to understand something quite well before you understand how simple it really is.

Anyways, I wrote it in Latex and compiled it into a nice little PDF so please follow the link below, it wouldn't look as nice in blog format.

https://www.simernes.com/docs/basics-of-bioinformatics-in-medicine.pdf

Information about Open Source Software in layman’s terms (Norwegian)

I recently did a write up trying to explain the concepts and incentives for writing and using Free & Open Source Software (FOSS). It's in Norwegian as the original thought was to shed light on what FOSS is for government officials and other decision makers that represent and affect me, so that they can have an easily digestible resource for understanding what it is. Feel free to comment and if you like the document or disagree or want to make an addition or amendment please follow the contribution instructions.

The document is available at www.simernes.com/open-source

Flashing Stock or Custom Firmware with Heimdall (on linux)

I had a bit of a learning curve when learning how to use Heimdall to flash images onto my phone (i9506, aka ks01lte) so hopefully this can help others with what I learned.

First of all, Heimdall is a flashing software for putting firmware into the different partitions of Samsung Android phones. It's cross platform, and supposedly equivalent in functionality to that of Odin, although I've never tried Odin. Heimdall is also cross platform so you can follow this guide if you're on mac or windows I think.

Heimdall basics
There are two executable programs:
1. heimdall
2. heimdall-frontend

I recommend using heimdall-frontend, but you need both because heimdall-frontend depends on heimdall.

Heimdall version
At the time of this post, the newest version was 1.4.2. I had to compile that myself from source though, but it was relatively easy if you just follow the build instructions inside the readme. I had to use 1.4.2 to get it to work with my phone so if you have issues you should try getting the newest one. There were binaries of 1.4.0 on the official website, and 1.4.1 in the ubuntu repo.

Installing Heimdall
At the time, I could also install heimdall from ubuntu repos with apt-get install, however the packages were called heimdall-flash and heimdall-flash-frontend. Idk why, but they're the same. Also they were 1.4.1 so they unfortunately didn't work for me, so I had to install them myself after compiling.

So briefly how to install it, although I'm not gonna give the whole command specific walk through as it is in the readme:
It's located at the github page:
https://github.com/Benjamin-Dobell/Heimdall

clone the directory:
git clone https://github.com/Benjamin-Dobell/Heimdall.git

Enter the directory and follow the build instructions as detailed (the last time I checked) at the very bottom of the readme file, specific for Linux, so it was inside the Linux folder.

Now after building you'll have two executable files:
heimdall
heimdall-frontend

The problem now is that you need to run these as root to connect to your phone, and heimdall-frontend uses heimdall, so you need to add them to your PATH.
However, by running sudo the PATH gets reset, so if you just export PATH=$PATH:$HOME/heimdalldirectory its not gonna find it so what I did (which you shouldn't really do because it should be reserved for system applications but whatever, it works, and you can just delete the heimdall files after you finished to keep a clean system) was to put both files in /bin/
sudo mv ./heimdall /bin/
sudo mv ./heimdall-frontend /bin/
Now you can sudo heimdall-frontend

Other problems with heimdall
If you get libusb errors when trying to export pid or anything else, try a different USB cable, and try different ports on your computer. That actually worked for me.

Flashing of firmware
First of all, your phone needs to be in Download mode, so google how you do that. For me I had to power off the phone, and then hold Power+Vol Up+Home. Or Vol Down I can't remember.

Then sudo heimdall-frontend and go to Utilities, and try to detect device. It should show a little messages saying it was detected.

Download and save .pit file
Next you'll want to Download the pit file from your device. This is also a good way to check if heimdall is working correctly, by just trying to print the pit. But you should really download the pit file and store it because you'll need it for flashing. It works as a sort of partition map (Partition Information Table).

So go ahead and download that and save it.

Now that you have that, you've done a very good job so pat yourself on the back. You're a really advanced hacker person aren't you? Wow. Good job. Now the real shit begins though so get ready. This is where you might brick your device so beware.

Really. Be careful. If you flash the wrong thing you're fucked so. Yeah.

Also, the warranty of your phone will be void after you flash anything onto it like this, so this is a kind of point of no return, although you might be able to flash it back to warranty condition if you have the stock recovery img. Not sure if phones can recognize that or not.

Flash custom recovery first
The first thing you might want to do is install a custom recovery like TWRP. TWRP lets you backup all your partitions, which can be nice in case you flash the wrong thing and want to get back to square one. You can also save your partitions with dd but I'm not gonna get into that here.
Like I said, this might void your warranty, and after doing this, I could not update through the stock phone update mechanism anymore (I mean, as a regular person going into Settings->about->Check for updates on your phone, it said something like "Your phone has been changed, no updates for you".

So to flash TWRP, open up heimdall-frontend again, go to the Flash tab, browse for your .pit file. Then Add a partition file, and select RECOVERY as the name, and find your recovery.img file: See figure 1.

Figure 1 -- heimdall-frontend with RECOVERY flashing

Now, start, and it will reboot when it finishes probably so be ready, and make it reboot straight into recovery right away. If not the custom recovery will be wiped. For me, booting into recovery was the same as to boot into download, just the opposite direction volume.

Now go into BACKUP and backup everything, and store that somewhere on your computer. In case something goes wrong. TWRP backs up to a directory on your phone located in /TWRP/Backups/.....

Flashing the rest of the firmware
Next, we'll be flashing some more interesting things. Like the full firmware, with modem and everything.

In my case I wanted to flash the newest stock rom update, because I needed the updated bootloader and modem firmware to install LineageOS 15.1 (Android 8.1), which I could later simply install from within TWRP.
So I downloaded the newest stock rom update from sammobile.
You can get the newest firmware from there for free if you sign up, but have to pay for older ones it seemed.
It might also be important that you get the right ROM for the right region or country, I don't know if that affects the ability for the phone to boot or not, but I'd try to get the right one if I were you.
For me it was a large file of about 1.5 GB. A .zip file to be exact, which upon extraction revealed two files, one of them being a .tar.md5 file.
If I just renamed the .tar.md5 file to a .tar file (removing the .md5 part of the name) I could extract it, and it revealed the files that can be flashed by heimdall.

In my case the files were:
aboot.mbn
boot.img
cache.img.ext4
hidden.img.ext4
modem.bin
NON-HLOS.bin
recovery.img
rpm.bin
sbl1.mbn
sdi.mbn
system.img.ext4
tz.mbn

Which made me very anxious and insecure, and I felt that this was perhaps a bit much, but then I figured it out.
Just like that recovery file from before, all these files correspond to a Partition name in Heimdall Frontend, from the .pit file. So what we'll actually do here with heimdall is just put the contents of these files/images into the partitions of our devices, and then they'll replace whatever was there from before. So it's all quite simple really if you think about it.
The name of the partition isn't always the same as the file, but there is a file name hint below the name so look at that. For example the APNHLOS partition name corresponds to NON-HLOS.bin. See figure 2.

Figure 2: APNHLOS file name hint

Now just keep adding all these until they're all in heimdall (figure 3). This should be a pointer also to whether or not you're using the right firmware. All files should fit into a partition. However, you might want to not flash the RECOVERY to preserve the custom recovery previously installed. You might have to boot directly into recovery again after flashing this time too to avoid reseting to the stock recovery, but I'm not sure. Just in case.

Figure 3: Heimdall Frontend with all firmware files added, except for the recovery image.

Now, if you dare, hit the Start button, and wait in excitement. Remember that your phone should be in Download mode right now. Also be sure to boot into recovery right away! And then just reboot, but your recovery might ask you if you want to remove the "Read only" permissioning, which I think you should do.

Great! That's it! Hopefully you didn't brick your phone. If you did, then hopefully you backed up with TWRP like I said before, and then you can restore it in TWRP. I think though that's just if you "soft bricked" and not "hard bricked", which is worse probably.

Good riddance! Thanks for reading. I hope it helped.

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Why this site exists

I made this site just because I wanted to have a website, so I don't really know exactly what to put here yet. I've done some app development, so I put that up and chances are that if you're visiting this site, you're either a robot or you came across one of my apps. Anyways, I'm glad you're here -- artificial or not -- so please, enjoy your stay.

Who knows, maybe when you read this the site has become copious in content.