Just to be sure, the issue is what to do with data that is in *pdb*
columns 79-80. The PDB Guide for HETATM, for example
(http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html), says:
77 - 78 LString(2) element Element symbol;
right-justified.
79 - 80 LString(2) charge Charge on the atom.
and the examples that it gives are:
1 2 3 4 5 6 7
8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 1357 MG MG 168 4.669 34.118 19.123 1.00 3.16
MG2+
HETATM 3835 FE HEM 1 17.140 3.115 15.066 1.00 14.14
FE3+
As to charges, I suppose 'charge' could be considered to be 'formal
charge' but also not unreasonable to consider 'ionic charge' or the
closely related 'oxidation number' or 'oxidation state'. The PDB example
seems likely to be closer to the latter than the former.
For the ATM type, the PDB guide cryptically says: 'Columns 79 - 80
indicate any charge on the atom, e.g., 2+, 1-. In most cases these are
blank.'
As I look at the 'Atom Block' of the *mol* file type, I see that field
'ccc' is designated as 'charge', for which values are '0 = uncharged or
value other than
these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 =
-3' , and Notes adds: '[Generic] Wider range of values in M CHG and M
RAD lines below. Retained for compatibility with older Ctabs, M CHG and
M RAD lines take precedence.
And further in the Properties Block is:
'M CHGnn8 aaa vvv ...
vvv: -15 to +15. Default of 0 = uncharged atom. When present, this
property supersedes all charge and radical values in the atom block,
forcing a 0 charge on all atoms not listed in an M CHG or M RAD line.'
[nn8 number of entries on line; value = 1 to 8; aaa atom number; value =
(1 to number of atoms)] and in an example:
M CHG 2 4 1 6 -1
FWIW, in the *CIF* core dictionary, '_atom_type_oxidation_number' is
defined as:
'Formal oxidation state of this atom type in the structure.' and 'The
permitted range is -8 -> 8 '
There is also '_chemical_conn_atom_charge', defined as 'The net integer
charge assigned to this atom. This is the formal charge assignment
normally found in chemical diagrams.', for which 'examples: 1, for an
ammonium nitrogen; -1, for a chloride ion' and 'The permitted range is
-6 -> 6'
> According to the comment that I put in JmolConstants.java a year or
> two ago:
>
> * This data is from
> * Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
> * (scanned for Jmol by Phillip Barak, Jan 2004)
>
> As I write this it occurs to me that perhaps there is some difference
> between "ions" and "charge" that I have misunderstood.
>
> The data that I have is for 'ionic radii' and contains radii for
> elementsin various ionization states. As I said above, other
> 'ionization states'
> are not allowed and revert to be uncharged (I *think* this is
> logged to
> the error log).
>
>
> I thought that ionization state and formal charge were the same
> things. If
> you folks tell me that they are not, then you can educate me and we
> canchange the implementation.
>
> Regardless, we need to do *something* so that people don't waste
> time on
> this and/or so that I don't have to keep explaining it.
>
> Let's keep talking.
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