This code is associated with the paper from Bozzi, Zimanyi et al., "Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter". eLife, 2019. http://dx.doi.org/10.7554/eLife.41124
python coarse-grained-ddmp.py structure_1 chain_1 structure_2 chain_2 helix_indices.txt offset
python coarse-grained-ddmp.py G45R A G223W A DraNramp_helices.txt 38
where inputs are:
G45R.pdb
G223W.pdb
DraNramp_helices.txt (Helix indices are inputted in new-line-separated text file, with both the beginning and end indices of each helix specified, i.e. there should be an even number of indices in the text file. Indices can be partially determined by DSSP, https://swift.cmbi.umcn.nl/gv/dssp/, but it may be best to curate the cutoffs of helices manually)
Offset is an integer referring to the shift of the first aligned residue, e.g. if the first aligned residue is residue 39, the offset will be 38.
Aligned FASTA of two sequences (G45R_A-G223W_A_aligned.fasta)
CSV of DDM (G45R_AvsG223W_A.csv)
PNG of DDM (G45R_AvsG223W_A.png)
CSV of coarse-grained DDM (G45R_AvsG223W_A-helices.csv)
PNG of coarse-grained DDM (G45R_AvsG223W_A-helices.png)