PROFASI  Version 1.5
Extracting parts of a PDB file

This is a utility to extract a portion of a given PDB file, like a particular model, one of the many chains, a certain range of residues in some chain, or only a certain kind of atoms. It works with the selection and filter rules as described in ProFASi PDB handling: Selections and Filters .


pdb_slices [OPTIONS] input.pdb:model:selections


pdb_slices abcd.pdb:5 -o model5.pdb

This would create a new pdb file model5.pdb with the 5th model in abcd.pdb.

pdb_slices abcd.pdb:5:A -o model5_chainA.pdb

This creates a new pdb file with the chain A of model 5 in abcd.pdb.

pdb_slices abcd.pdb::A,2,30 -u "+BB+CB" -o bbcb.pdb

This uses the residues labeled 2 through 30 in chain A of the first model in abcd.pdb. Only backbone and C-beta atoms are present in the new pdb file.

pdb_slices abcd.pdb::A,2,30 -u "+BB" -r atom_index -o new.pdb

In this case, the atom numbers in the new pdb file will be 1,2,3..., instead of whatever numbers the selected atoms had in the original file. Similarly, to have residues renumbered from 1, replace atom_index with residue_index. To have both renumbered, use "-r atom_index\&residue_index".

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2