1. cut only pore region and optimize aa range for human, mouse, and 6O72 structures 
   (it appears that aa range 650-710 is crucial for proper alignment!).
   Run the following comand in Chimera:
	del :1-654 | :1010-5000 | ligand

2. Delete TERM sections from pdb files with the following bash command
   (for comparison of whole pore/TM region and not just a single chain in PDB 'TER' sections has to be removed!)
	for f in *.pdb; do grep -v ^TER $f > ${f%.pdb}-TER.pdb; done

3. Align sequences with frtmalign software:
	for f in input_files/*.pdb; do ./frtmalign $f 6co7_6co7_tmem_align.pdb > ${f%.pdb}_output.txt; done

4. Add aligned sequences to MSA from Huffer et al (selected ones);
   align all sequences to a single 6CO7 reference, remove insertions and N- and C-terminal flanking regions






	
