Re: [Jmol-developers] custom radii for charged atoms

[Miguel <mi...@jm...>]

>> Phil wrote:
>>
>> > ... I honestly can't see that there is a need to force a
>> > special radius for that N...neither for calculating bonds nor for
>> > spacefill display...since the formal charge doesn't enter into those=

>> > matters at all.
>>
>> I'm getting more confused.
>>
>> The formal charge *does* enter into the bonding radius.
>
> Not to the best of my understanding, and I'll dare to argue with the
> code-meister.
>
> As I know it, as currently implemented in Jmol, the charge listed in pd=
b
> column 79-80 is taken as ionic charge, or oxidation state, of that atom=
,
> then compared against a table of ionic radii.

Basically correct ... with the exception that I would use the phrase
'formal charge' where you are using 'ionic' ... perhaps that is erroneous=
.

> If a match in charge is
> found, then that ionic radius is used in the bonding-by-proximity
> calculations and spacefill ionic display.

Correct

> (And we learned over the past
> year, that bonding-by-proximity calculations with Fe3+, Al3+, Si4+,
> etc., fail b/c the radius of the neutral atom is _way_ too different
> than the ionic radii and therefore way too big and therefore creates
> 2x-4x extraneous bonds, and impossible bonds at that.)

Agreed

> To make it clear, from the chemistry side, the table of radii has
> *nothing* to do with formal charge and everything to do with ionic
> charge.

Then apparently I have a fundamental flaw in my model ... and in the Jmol=

implementation.

I thought that ionic =3D=3D formal charge and the implementation reflects=
 that.

> Sometimes the ionic charge and the formal charge (btw, usually
> zero on most atoms, but most common non-zero values I would guess to be=

> +1 and -1) may be identical values on a particular atom, but most often=

> not. As I stated before, the PDB Guide's example of the charge field
> certainly leads one to believe that the ionic charge, or oxidation
> state, was the intent of the format, hence MG2+ and FE3+ in the example=
.

OK.

I previously said that the PDB file contained a 'formal charge' because i=
t
was pretty clear that it was not a partial charge and I thought that ther=
e
was only one other thing ... a partial charge.

> Getting back to the start point on this issue, the original petition wa=
s
> simply that  charges that don't have a match in the ionic radius table
> don't get overwritten with zero.

Yes, I can do that.

> And that should be fairly simply
> accomodated without upsetting the cart on all the good things that can
> be done with the ionic charge in cols 79-80.

Correct. I can keep the charge value, allow its use for display purposes,=

use the bonding radius for the uncharged atom, and not look into it any
deeper. That will solve the short-term issue.

That does leave open the longer-term issue of my fundamental confusion
between ionic charge and formal charge.

> More questions? How about a phone call?

Can't do it today ... perhaps next week.


Miguel