Pdbset (ccp4)

pdbset — is part of the ccp4 package and has various useful manipulations on coordinate files (e.g., PDB files).

Syntax

pdbset XYZIN foo_in.pdb XYZOUT foo_out.pdb
[Keyworded input]

Keyworded input

• The available keywords are:

BFACTOR, CELL, CHAIN, COM, ELEMENT, EXCLUDE, OCCUPANCY, ORTHOGONALIZATION, OUTPUT, PICK, REMARK, RENUMBER, REORTHOGONALIZE, REPLACE, ROTATE, SELECT, SEQUENCE, SHIFT, SPACEGROUP, SYMGEN, TRANSFORM, UTOB, XPLOR, NOISE, ATRENUMBER

Example usage

#!/bin/sh -f
pdbset xyzin input.pdb xyzout output.pdb << eof
OCCUPANCY RESET 90
BFACTOR ALWAYS 0
eof

Or,

echo "BFACTOR ALWAYS 0" | pdbset xyzin input.pdb xyzout output.pdb

Extended examples

Note: These were taken directly from the man page.

########################  Convert PDB file to mmCIF format
#!/bin/csh -f
#
pdbset xyzin toxd.pdb xyzout toxd.cif << eof-1
output cif
end
eof-1

########################  Take output from O into a form suitable for refinement
#!/bin/csh -f
#
pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1
cell    132.02  115.21   96.20   90.00   90.00   90.00
spacegroup P212121
eof-1

###################  Take output from Xplor into a form suitable for refinement
#!/bin/csh -f
#
pdbset xyzin bst_113m.pdb xyzout temp1.pdb << eof-1
cell    132.02  115.21   96.20   90.00   90.00   90.00
spacegroup P212121
xplor
eof-1



######################## Expand dimer to tetramer, rename chains, transform
#!/bin/csh -f
#
#  Make tetramer from dimer
#
pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb <<eof-1
remark  Tetramer generated from AB dimer
remark   rotated to pqr frame
remark
! Generate other dimer by z-dyad in P21212
symgen  x,y,z
symgen -x,-y,z
! Rename chains in second dimer: V & W are water chains
chain symmetry 2   A C
chain symmetry 2   B D
chain symmetry 2   V X
chain symmetry 2   W Y
! transform to molecular frame
transform -
  0.87831   0.47808   0  -
    0         0     -1.  -
 -0.47808   0.87831   0  -
 0.0  -2.713  0.0
eof-1

External links

• pdbset man page