Barnaba usage for kink-turns in Python with custom pdb files

[theoboury]

Hi, I want to use Barnaba to compare kink-turns between them and also with some new other patterns.

I would like to obtain first eRMSD values between two kink-turns. So I relied on the file example_07_double_strande.ipynb from this git.

Here is the script that I used:

import barnaba as bb

query = "../test/data/1.txt" 
pdb = "../test/data/1S72.pdb" # Here 1S72.pdb is supposed to be replaced by another kink-turn file, but the bug already appeared with this setup.
(l1, l2) = (5, 7)
# call function. 
results = bb.ds_motif(query,pdb,l1=l1,l2=l2,bulges=0,threshold=0.7,out='motif')

I put as additional files both the error (error.txt) and the kink-turn pdb file (1.txt). I think the problem comes from my file 1.txt as I generated it from a custom parser from a RNA graph.

Indeed, when I tried to compare it with the git examples (SARCIN.pdb and 1S72.pdb, with the latter that can be reduced to only the lines containing ATOM), I cannot find any difference. Can you please say me if you see any problem with my 0.pdb file or any other problem that can be fixed ?

Thanks a lot and have a nice day, Best, Théo Boury

1.txt error.txt