Pdbset (ccp4)
From Christoph's Personal Wiki
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