PDB_MERGE (CCP4: Supported Program)
NAME
pdb_merge
- merge two coordinate files into one
SYNOPSIS
pdb_merge xyzin1
foo1_in.pdb
xyzin2
foo2_in.pdb
xyzout
foo_out.pdb
[Key-worded input file]
pdb_merge can be used to merge two coordinate files into one. The
program currently has two modes:
- merge chains
- The residue and chain labels in XYZIN1 and XYZIN2 are taken as is, and
transferred to XYZOUT. This means that if both input files have a chain A,
then XYZOUT will have a chain A containing all the atoms from both
input files. If you want e.g. to join two domains into one chain, then
this might be what you want. But if the input chains are not prepared
correctly, then you may have residues with duplicate atoms.
- nomerge
- For this option, it is assumed that chains in XYZIN1 and XYZIN2 are
distinct from each other. Therefore, if a chain label is found in XYZIN2
that is already used in XYZIN1, then it is relabelled. For example,
if both XYZIN1 and XYZIN2 contain chain A, then XYZOUT will contain
chain A (from XYZIN1) and chain B (from XYZIN2).
If you want to merge more than 2 files, then pdb_merge should
be run iteratively.
INPUT AND OUTPUT FILES
XYZIN1
First input coordinate file. The input format is detected automatically (PDB, mmCIF
or MMDB).
XYZIN2
Second input coordinate file. The input format is detected automatically (PDB, mmCIF
or MMDB).
XYZOUT
Output coordinate file, in format selected by OUTPUT
keyword (default PDB format)
KEYWORDED INPUT
Specify the nomerge option, see DESCRIPTION above.
The default is to merge chains with the same chain label.
(default is PDB)
Select output file format: PDB = standard PDB format, CIF = mmCIF format,
and BIN = MMDB binary format.
END
End keyworded input.
PROGRAM OUTPUT
The program currently gives a short summary of the commands received.
SEE ALSO
ffjoin
AUTHOR
Martyn Winn, Daresbury Laboratory, UK