PDB Tools
for Modifying Existing PDB Files

Updated September, 2004

PDB-Editing Capabilities & Limitations of RasMol, Chime, WebLab, Swiss-PDBViewer

Information in this table was determined by Eric Martz. Please communicate corrections and additions to him. Information for Swiss-PDBViewer was kindly provided by Nicolas Guex, its creator.

Property RasMol 2.6 beta-1a MDL Chime WebLab Viewer 2.01 Swiss PDBViewer/DeepView
Method Evaluated Command "save pdb <filename>" Menu: File, Save Molecule As. Menu: File, Save As, PDB (see note 1) Menu: File, Save As. and Menu: File, Save Selected Residues.
Misc. Header/remarks lost. Header/remarks retained; original PDB file unmodified. PDB file severely damaged: Some residue names changed (HOH becomes UNK or MOL). All temperature factors lost. Header/remarks lost. Header/remarks lost. Temp factors retained (might be set to 99.99 if residue was mutated). Solvent (HOH, WAT or H2O) saved only if it was loaded (there is the option to ignore solvent atoms in the preferences).
Able to save subset of atoms Yes (selected atoms). No. Yes (see note 1) Selected residues: (Menu) File, Save Selected Residues.
Atomic Coordinates Unconditionally changed to new arbitrary center different for each subset of atoms. Original coordinates unconditionally preserved. Original coordinates unconditionally preserved. Original coordinates preserved if option Save in Original Orientation of the File menu is enabled. Else rotated/translated coordinates are saved.
CONECT records Lost. Preserved. Lost. Preserved. Created if was not present in the input file.
Rotation. Ignored. Ignored. Ignored. Version 3.51: Original coordinates preserved if option Save in Original Orientation of the File menu is enabled. Else rotated/translated coordinates are saved. Versions 3.6, 3.7 always save original unrotated coordinates.
User center Ignored. Ignored. Ignored. Kept if "Save in Original Orientation" of the File menu is disabled.
Atom serial numbers Unconditionally renumbered. Preserved. Unconditionally renumbered. Unconditionally renumbered. Note that Residues and chain numbers can be changed as you wish from the "Rename Current Layer" item of the "Edit menu".

  1. Free WebLab Viewer Lite and the commercial WebLab Viewer Pro were offered by Molecular Simulations, Incorporated (MSI). MSI was subsequently acquired by Accelrys which offers a commercial version only of what used to be WebLab, now renamed Accelrys Viewer. (WebLab Viewer 2.01: To save a subset of the atoms, select the atoms, then Edit, Copy, then File, New, then Paste, then File, Save. During the save you will have two windows open, one with all atoms and one with the subset.)

Martz-Authored PDB Tools

These small programs were written in C. One initial application was to extract subsets of atoms from large PDB files of lipid bilayers. Subsequently, others were developed to make morphs.

Detailed documentation is in pdbtools.txt and the programs themselves are available (both as DOS executables and as C source) in the zipped file pdbtools.exe.

Feedback to Eric Martz.