The goal of FragmentSelector is selecting a fragment from a protein. The requirements for the resulting fragment are:
- The fragment should contain the atom A and its closest surroundings, i.e. atoms within the radius r.
- The number of bonds broken by the selection should be minimal.
- The number of atoms in the fragment must not be higher than N but should be as close to N as possible (this is less important than the previous requirements).
An input of the program is a PDB file containing a protein and the parameters A, r, and N. Parameter A can be one atom or a set of atoms specified by an atom query string (see Remarks). Other parameters can be set by options. The output is a file containing atoms of the selected fragment in PDB format. (The output file will only contain ATOM and HETATMS records.)
- .NET Core 3.1 (
dotnet) - PyMOL (
pymol) - only if you want to use-roption
All files needed for execution are found in directory release/.
Print version and help message:
dotnet release/FragmentSelector.dll
Cut fragment with at most 500 atoms around atom 3810 in data/1tqn.pdb with required radius 10 Angstroms. Save result in data/1tqn.fragment.pdb:
dotnet release/FragmentSelector.dll data/1tqn.pdb 'id=3810' 8 500 -o data/1tqn.fragment.pdb
The same, but use algorithm mode 1, print partial result from each step, and create a PyMOL session with visualization of the results:
dotnet release/FragmentSelector.dll data/1tqn.pdb 'id=3810' 8 500 -o data/1tqn.fragment.pdb -m 1 -s -r
Using the -r option (create PyMOL session) requires that PyMOL be installed on the system, and that release/config.txt contain the path to the PyMOL executable.
Multiple options must not be grouped together (e.g. -s -r cannot be shortened to -sr).
Atom query string can be used as the 2nd parameter to specify more than one central atom. This string can specify chain ID (chain), residue number (resi), residue type (resn), atom name (name), and atom ID (id). Examples:
'chain=A&resi125'
'chain=B&resn=ALA&name=CA'
'id=3810'
Quoting the atom query string is recommended (& is a special character in bash).
Details can be found in this work:
- MIDLIK, Adam. Selection of protein fragments using minimal bond breaking [online]. Brno, 2014 [cit. 2021-03-18]. Available from: https://is.muni.cz/th/pqum6/. Bachelor's thesis. Masaryk University, Faculty of Informatics. Thesis supervisor Radka Svobodová.