PDB-Editing Capabilities & Limitations
of RasMol, Chime, WebLab, Swiss-PDBViewer
Information in this table was determined by
Please communicate corrections and additions to him.
Information for Swiss-PDBViewer was kindly provided by Nicolas Guex, its
|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".|
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.