**ATOM OVERLAP CHECKER README**
If you are using this script please acknowledge me (Dr Owen Vickery) and cite the following DOI.DOI: xxx
**ATOM OVERLAP CHECKER, SCRIPT OVERVIEW**
This script finds and atoms which are within a set distance and will move them until they are beyond the cutoff.
**REQUIREMENTS**
Software:
- Python v3 or higher
Non standard python modules:
- Numpy
- Scipy
Standard modules included in base python install (ubuntu 18):
- os
- sys
- itertools
**FLAGS**
REQUIRED
- -f input (pdb)
- -o output (pdb)
- -overlap (float)
The script only works with pdb files.
using the flag -f for the input file -o for the output file. The flag -cutoff overwrites the default 0.4 A cutoff.
python check_atom_overlap.py -f input.pdb -o ouput.pdb -cutoff 0.5
The above command will fix any overlaps within 0.5 A.