The following information applies to RasMol version 2.6-beta-2a and Chime 1.0 or 2.0. It does not address any relevant changes which may have been made in RasMol 2.7 or later.

The bottom line is that, by default, for macromolecules, RasMol and Chime use internal algorithms to determine the placements of all covalent bonds. For macromolecules, in nearly all cases, the CONECT records in the PDB file are ignored. However, this default behavior can be adjusted as explained below.

What are the values used by RasMol and Chime for van der Waals radii in the spacefill rendering?

The radii for common elements are listed below. If the PDB file contains hydrogen atoms, the van der Waals radii are used; if not, slightly larger 'united atom' radii are used for C, N, O, and S as detailed below.

Chime or RasMol can be forced to use van der Waals radii (instead of united atom radii) for spacefill and dots by adding a single hydrogen atom to the PDB file with a text editor, a line such as

HETATM 9999  H                   0.000   0.000   0.000  1.00  1.00

Roger Sayle states

Most protein structures in PDB do not contain explicit hydrogens as these are not resolved by X-ray crystallography. As a result for molecules without hydrogen atoms, RasMol uses 'united atom' Van der Waal's radii for carbon, nitrogen, oxygen and sulphur. This is the effective size of an atom plus its hydrogens (commonly used in forcefields and a better approximation of the molecule's surface).

Note that the increase for carbon is larger than for oxygen, this is caused by both the average number of aditional hydrogens and how closely they're bound to their parent atom.

Unfortunately, RasMol does not maintain a table of ionic radii for each possible charge state of an element, and so the values used by RasMol for displaying salts or similar structures are incorrect. Complete and reliable tables of ionic radii are both rare and harder to encode in computer software. For example, the CRC handbook lists five ionic radii for selenium: -2 (1.91A), -1 (2.32A), +1 (0.66A), +4 (0.50A) and +6 (0.42A). This series fits well with the VdW radius (as used by RasMol) of 0.9A in the uncharged state.

The complete set of radii may be found in RasMol's source code, in the file abstree.h. The values are given in RasMol units, for example, 387 for carbon. One Angstrom equals 250 RasMol units.

How do RasMol and Chime determine which atoms in a PDB file are covalently bonded?

The first decision made by RasMol/Chime is whether the PDB file itself specifies the bonds. Bonds are specified in PDB files with CONECT records.

• If the number of bonds specified in the PDB file's CONECT records is greater than or equal to (atoms + heteroatoms - chains) then the PDB-specified bonds are shown. (This is commonly the case for small molecules, and rarely the case for macromolecules.) This behavior can be overridden with either the connect command, or the set connect command (see below).

• If the above criterion is not met, RasMol discards all single-bond CONECT information in the PDB file and assigns all bonds itself, using one of the following methods. This is the usual case for macromolecules.
  • If (atoms + heteroatoms) exceeds 255, RasMol uses a simple and quick method of assigning bonds designed for large biological molecules. This method can be forced on any loaded structure with the command connect false. Two atoms are considered bonded when the distance between them is between 0.4 and 1.9 Angstroms, unless one or both atoms are hydrogens, in which case the bonded range is between 0.4 and 1.2 Angstroms.

  • If (atoms + heteroatoms) is less than or equal to 255, a more time-consuming algorithm is employed. This algorithm can be forced on any loaded structure with the command connect true. Two atoms are considered bonded when the distance between them is between 0.4 Angstroms and (the sum of their covalent radii plus 0.56 Angstroms). The covalent radii employed for all elements can be found in the source code. Those used for the most common elements are shown above.

    Covalent Bond	Bond Length	Maximum Length Allowed by RasMol/Chime (<255 atoms or connect true)
    C-H	1.06-1.11 Angstroms	1.60 Angstroms
    C-C	1.5	2.00
    C-N	1.3-1.5	1.96
    C-O	1.4	1.96
    C=O	1.2	1.96
    "P-P"		2.632
    P-O		2.276
    S-S	2.04	2.60
    S-O		2.26
    Ca-O		2.232
    Zn-S		3.028

• The above description describes the default behavior of RasMol or Chime, which is equivalent to the command set connect true. The command set connect false, which must be issued before loading the PDB file, instructs that only bonds specified in CONECT records are shown; no bonds are assigned by RasMol or Chime. Since CONECT records in macromolecular PDB files obtained from the Protein Data Bank specify bonds only for hetero atoms and hetero groups, this results in no bonds being shown for most of the atoms in such files. It is appropriate for small molecules in which all bonds are specified by CONECT records.

• For macromolecules, the bond-assignment behavior of RasMol offers no mechanism for adding arbitrary bonds, short of specifying all bonds in a macromolecule in the CONECT records, a task not easily accomplished in a PDB file with thousands of atoms. The most common example of arbitrary bonds which need to be shown are the hydrogen bonds not in the backbone-only subset which RasMol shows on request.
  • A workaround in RasMol is to use the monitor command. This allows dotted lines to be drawn between arbitrary atoms. The disadvantage is that these are always single-pixel lines and cannot be rendered as solid cylinders of specified radius as for real bonds (using the wireframe command, e.g. wireframe 0.15).

    For example, if you wish to show hydrogen bonds between atom serial numbers 117-214 and 117-303

    set monitor off # optional; hides distance label
    monitor 117 214
    monitor 117 303

  • In Chime 2 only, a new command allows addition of arbitrary bonds with CONECT records which must be added to the end of the PDB file. The command set connect save (which must be issued before loading the PDB file) forces Chime 2 to show bonds for all CONECT records in the PDB file, while at the same time calculating bonds not specified in the CONECT records in the usual manner (described above). The command can also be issued in the embed tag which invokes Chime (see Programming Chime Web Pages from Scratch). Rather than using the script parameter in the embed tag, in order to execute the command before the molecule specified by the src parameter is loaded, use the initscript parameter, for example:
    <embed type="chemical/x-pdb"
    src="1hho.pdb"
    height="50%" width="50%"
    initscript="set connect save">

  (As of August, 1999, set connect save and initscript have not yet been documented in MDL's Chime 2 documentation, nor is the former documented in the Chime 0.99 partial draft manual which documents some of the commands not yet documented by MDLI.)

Hiding Arbitrary Bonds

Hiding arbitrary bonds is a straightforward application of commands adequately documented in the RasMol Reference Manual. One must either select the unwanted bonds, and then issue the command wireframe false, or else "restrict not" the unwanted bonds. Bonds are selected or restricted by selecting or restricting the atoms at the ends. Hence restricting bonds will also hide spheres, while selecting bonds followed by wireframe off will preserve spheres.

By default, atoms at both ends of a bond must be selected to operate on that bond. This is equivalent to the command set bondmode and. Alternatively, after issuing the command set bondmode or, commands operate on all bonds for with an atom at either end is selected.

Hydrogen Bonds

The hbonds command displays only backbone-to-backbone hydrogen bonds in regions of defined secondary structure, and Watson-Crick inter-nucleotide bonds in DNA double helix. RasMol and Chime have no built-in mechanism to locate and display other types of hydrogen bonds, such as any involving sidechains, inter-chain hbonds, ligand-protein hbonds, etc. The Noncovalent Bond Finder, a tool which employs Chime, can be used to visualize hbonds involving any selected set of atoms. For small ligands, contact surfaces provide an overview which highlights the hbond locations, and the atoms involved. A user-friendly method for generating contact surfaces is provided in the Protein Explorer.

For protein, regions of alpha helix or beta-sheet are identified by application of the algorithm of Kabsch and Sander. Hydrogen bonds are assigned when a distance-dependent electrostatic energy of interaction between donors and acceptors falls below a threshold value. No reference is made to phi or psi angles.

For DNA, Watson-Crick double helix internucleotide bonding rules are applied without reference to actual distances between donors and acceptors. This can lead to gross errors. For example, in 1d66.pdb, cytosine 28 was positioned erroneously (Ronen Marmorstein, personal communication). Two impossible hbonds are drawn, disregarding the actual geometry. One hbond is drawn from G11.N2 to C28.O2 across one intervening bond and one intervening atom, a distance of 7 Angstroms! (Hbond donor-acceptor distances are generally less than 3.5 Angstroms.)

CONECT Records

The full specifications for CONECT and all other records in the PDB format are available at the PDB. (While the mmCIF format was recently adopted as the new international standard for atomic coordinate files, neither RasMol 2.6 nor Chime 2.0 can read mmCIF. RasMol 2.7 can read mmCIF but is not documented here.) According to the PDB format, CONECT records are not required for the 20 standard amino acids nor for the 5 standard nucleotides. (Alas, the PDB residue naming standard makes no distinction between the ribo- and deoxyribo- forms of nucleotides.) CONECT records are required only for hetero atoms. Since this means that the number of bonds specified by CONECT records in PDB files obtained from the Protein Data Bank is always far less than the number of atoms for proteins and/or nucleic acids, RasMol and Chime always ignore the CONECT records unless instructed to do otherwise with a set connect false or set connect save command prior to loading.

The record identifier is spelled "CONECT" (rather than having two N's) because the identifier word is limited to 6 characters. Take for example:

CONECT    2    0    3    0    0

CONECT    3    2    4    8   33

CONECT    2    3

RasMol and Chime support a mechanism for specifying double or triple bonds in CONECT records which is not part of the official PDB standard. The PDB format standard makes no provision for specifying double or triple bonds.

According to the PDB format standard, only the second through fifth numbers in a CONECT record designate covalent bonds. The sixth and later numbers designate hydrogen bonds and salt bridges. However, RasMol and Chime interpret as covalent bonds up to six numbers per record, namely those in the second through seventh places. RasMol and Chime ignore any hydrogen bonds or salt bridges specified in the eighth position through the eleventh and final position.

Information in this document was gathered from the history of the RasMol EMail List (mostly from information contributed by Roger Sayle), from tests of RasMol and Chime, and from RasMol's C source code.

Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983.

Carey, Francis A., 1996, "Organic Chemistry, Third Edition", McGraw-Hill, New York.

Engh R A & Huber R (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst., A47, 392-400.

ProCheck (Biotech Validation Suite for Protein Structures).

Source code references

The function which assigns bonds to pairs of atoms is Testbonded() in molecule.c.

Covalent and van der Waals radii are in the structure ElemStruct in abstree.h.

For protein backbone hbonds, see CalcProteinHBonds() in molecule.c, or search for "Kabsch".