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Porcupine plot generation automation (PORCUPINEplot)

PORCUPINEplot is a script developed to automate the generation of porcupine plots of PCA analysis.

To use this program, first you need to calculate the Principal Components (PCs) of the protein trajectory. Feel free to check and use the PCA program I also developed over here.

To create a Porcupine plot, you are going to need the protein structure (pdb file) and the PC trajectory file (dcd file). You may also use other extensions for structure (gro) and trajectory (xtc) but you are going to need to change ln 13 of porcupineGenerator.sh to:

if ls -l *.{gro,xtc};

Instalation

Download the code and unzip it on the desirable directory. To prepare the environment use the following command:

conda env create -f environment.yml

Be aware to uncomment the sections on the environment.yml file depending on which OS you are using.

How to use

Activate the environment using:

conda activate porcupineplot

The program uses a shell script to automate the calculation of data in multiple folders. To use this feature go to the root directory and on the terminal use:

bash \porcupineGenerator.sh

If you are interested only on running one folder, you may just add your files to the porcupineGenerator directory and use:

pymol script.pml

Before running the program, be aware to do some edits to the script.pml file:

```

---------------START-------------------------------------------------

Change this filename to the name of your archive

load pc0.pdb load_traj pc0.dcd run modevectors.py

Change the 10001 to the number of frames the traectory has

split_states pc0, 1, 10001

Change the name 'pc0_0001' to the name of your filename

Here you can also format the porcupine plot

modevectors pc00001, pc010001, cutoff=.0, headlength=2, head=0.4, headrgb=(1,.2,.1) ,tailrgb=(1,.2,.1) ,notail=0 set cartoontrace,1 set cartoontuberadius, 0.3 cmd.disable('all') cmd.enable('pc00001',1) cmd.enable('modevectors',1) set rayshadow,0

Change the name of the session file

After that, you may save as PNG

save PCAporcupinepc0.pse,format=pse

----------END------------------------------------------------

```

Observations

• This script was developed following the SK D tutorial on youtube, the PML file was developed based on its PML file. The tutorial and files can be found here.

• The file modvectors.py was developed by Sean M. Law and its description can be found here

Authorship

• Author: Brenda Ferrari (brendaferrari)

Social preview original photo by Brenda Ferrari (brendaferrari)