mTM-align

Download the zip file from the website:

wget http://yanglab.nankai.edu.cn/mTM-align/version/mTM-align.tar.bz2

Decompress the file:

tar -xf mTM-align.tar.bz2

A folder with the name mTM-Align will be created. Enter the folder and run:

cd src && m|e && cd ..

Now the program is ready to be used.

Export the PATH so you can run it from your local directory:

export PATH="/home/mTM-align/mTM-align/src:/$PATH"

mTM-align -i <input_list> -outdir <output_folder> -o <superpose_image>

The input_list is a file containing the full path of all PDB files you want to align. Example:

/home/Structure/PDB/2519103099_2519473577_Methanolobus_psychrophilus_R15_b205d_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
/home/Structure/PDB/PDB/2558309039_2558444101_Megasphaera_elsdenii_T81_cf13c_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb
/home/Structure/PDB/PDB/637000327_637160692_Treponema_denticola_ATCC_35405_519cf_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
/home/Structure/PDB/PDB/XP_0240649571_a559b_unrelaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb

To create this input file, go to the folder where the PDB files are and run:

ls > input_file

To add the path to the beginning of each line, run the following command, replacing /home/info/ with the path where your file is:

sed -i s'#^#/home/info/#' file

Your structure alignment is in the file result.fasta. This file can be used as input to generate a phylogenetic tree in any program, for example IQ-TREE.

Two other important output files are the pairwise alignment tables pairwise_rmsd and pairwise_TMscore. These files report the quality of the alignments as numerical scores and should be processed and combined in a spreadsheet.