pdb_select set1,set2,set3,... < orig_pdb_file > new_pdb_file
This command creates a new_pdb_file containing a subset of residues from the orig_pdb_file. The only argument to pdb_select is a comma-separated list (no spaces) of sets of residues in Chimera/ChimeraX format. (The selection syntax is described below, as well as in the Midas/Chimera documentation). "new_pdb_file" will contain residues belonging to the union of all the sets (set1, set2, set3, etc.).
set residues selected:
-------- ---------------------
"100" all residues whose seqNums are 100
"100-150.A" all residues in chain A whose seqNums are in [100,150]
"*-150.A" all the residues in chain A whose seqNums are up to 150
"150-*.A" all the residues in chain A whose seqNums are at least 150
"*.A" all the residues in chain A
".A" " " " " " "
"100-150.A-C" residues 100-150 in chains A through C
"100-150.*" residues 100-150 in all chains
"100-150." " " " " " "
"100-150" " " " " " "
"*.*" the entire molecule
"." " " "
If you use the '*' character in any of your sets, you will have to enclose the first argument in quotes to circumvent the shell.
- Only the ATOM, HETATM, ANISOU, HELIX, SHEET, and TURN records are effected. All other records in the PDB file are blindly sent to the standard output.
- Helices, sheets, or turns which lie all, or partially outside the selected sets of residues will be deleted.