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

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".

Notes:

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

• SPLIT.EXE splits large files into smaller pieces. (Can be reassembled with the DOS copy command.)
• ACORN.EXE is the Atomic COordinate ReNumbering utility.
• NEWCHAIN.EXE inserts or replaces a chain designation character into a PDB file.
• CORSEL (COoRdinate SELection) selects atoms in a given range of coordinates, and/or reports the minimum and maximum X, Y, and Z coordinates present.
• STRIPH removes hydrogen atoms from a PDB file.
• ALPHAC discards all atoms except alpha carbons, phosphorus atoms, and hetero atoms.
• MORPH2 generates a series of interpolated frames between two PDB files. The PDB files must match, atom by atom, in the same order. The interpolation is linear: each atom "moves" in a straight line between its start and end positions. The original pair of PDB files and the interpolations are concatenated into a single PDB file, delimited by MODEL and ENDMDL records, which is ready to play as an animation in Protein Explorer (examples).

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.