Calculating missense constraint within protein tertiary structures. The following provides information on how to run each script.
You will also need to download the following, and set the paths within the R script accordingly:
LiftOver executable
You will need to make a free educational account and sign in to download the executable.
Add to cart the LiftOver program https://genome-store.ucsc.edu, click Login/Register in the top right, follow the instructions then check out.
LiftOver chain file
wget -c http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
GENCODE GTF file
wget -c http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz
Run for any given PDB file with a single chain (Chain A)
Rscript pairwise_distances.R <my pdb structure> <my output text file>
Rscript pairwise_distances.R AF-Q969H0-F1-model_v1.pdb AF-Q969H0-F1-model_v1_distances.txt