Setup

This guide will describe how to set up an environment using micromamba, but conda or mamba are also fine. Micromamba seems to be the fastest.

To install micromamba (Reference):

# If on the VSC:
cd $VSC_DATA

curl -L micro.mamba.pm/install.sh > install_micromamba.sh
bash install_micromamba.sh

This should show you a step-by-step wizard:

Micromamba binary folder? [~/.local/bin] -> Default is fine
Init shell (bash)? [Y/n]                 -> Default is fine (may be different based on your default shell)
Configure conda-forge? [Y/n]             -> Default is fine
Prefix location? [~/micromamba]          -> Change, see below

Important: When asked for a "root prefix", you can choose:

• .micromamba, without the ~ at the beginning. This will create one folder named .micromamba where you currently are, which contains the default environment. When you create a new environment while inside a project, it will create a new .micromamba folder inside that project for your new environment.
• /some/absolute/path/micromamba: This will create one directory that will hold all your environments. You can echo $VSC_DATA/micromamba and then copy that.

By default, micromamba creates environments in the home directory. You don't want that on the VSC or you'll run out of quota. The .micromamba directory is gitignored in the protein-runway project, so it's a fine choice. It's also okay to choose $VSC_DATA/micromamba or whatever you like inside of $VSC_DATA, just make sure to expand it beforehand.

Set up and activate a protein-runway environment from the env file in the repo:

micromamba create -f micromamba_env.yml
micromamba activate protein-runway

Arguments:

• -n protein-runway: Name of the environment
• -c conda-forge: Source for installing dependencies
• python=3.11: Install a standalone python so we can be independent from the VSC python

Install dependencies:

pip install -r requirements.txt

Annoyingly, this will likely still show some dependency errors, but they don't seem to stop the pipeline from working.

Run snakemake

Before running any code, we need to activate the micromamba environment:

micromamba activate protein-runway

The input data consists of two files per protein from Zenodo https://zenodo.org/records/4650406:

• Trajectory file from Trajectory_snapshots_<code>_<code>.zip:
  • e.g. 1fuu_noPTM_10-20ns_100snap.trr
  • Location: 01_input/traj/
• Topology file from Topology_stripped.zip:
  • Example: 1fuu_noPTM_complex.top
  • Location: 01_input/top/

At that point, snakemake -call should build all necessary output files for these proteins into 03_output.

Build blender extension

You need to install packages and zip them. To install, this should work from the root of the project:

pip wheel mdanalysis -w ./blender/extension/wheels/

Then zipping the extension can be done by running:

bash blender/build.sh

But this assumes you're on Linux or Mac, so you can just take the contents of the "blender/extension" folder and zip them manually. You can then install the addon from Edit > Preferences > Get Extensions. Then, in the right-hand corner menu, Install from Disk.

What blender does then is it just unzips that into a local folder. For me, that folder is ~/.config/blender/4.2/extensions/user_default. So if you want, you can symlink the extension directly there, so that when you edit the code, you can just re-launch blender. For me, the directory looks like this:

% ls -al
total 12K
drwxr-xr-x 3 andrew andrew 4.0K Nov 12 20:47 .
drwxr-xr-x 6 andrew andrew 4.0K Nov 12 20:02 ..
drwxr-xr-x 3 andrew andrew 4.0K Nov 12 20:41 .blender_ext
lrwxrwxrwx 1 andrew andrew   55 Nov 12 20:47 protein_runway -> /home/andrew/projects/protein-runway/blender/extension/

Again, if you're on Windows, you can't do symlnks, as far as I know. But you could edit that folder and then copy the changes back to the project so you can commit them into git. There might be other ways to work on the project easily.