Dear Ian,
I think this is a very good suggestion. I had been thinking myself on adding a 'multiplicity column' to the mmCIF, which would indicate whether the refinement program had assumed a true special position or a rotated disordered molecule. However, this would require that all programs using the mmCIF would have to be rewritten, so I think your solution is much better.
Best regards,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Ian Tickle
Sent: Friday, December 17, 2010 1:06 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I thought about this and I think the only workable solution that will keep everyone happy and maintain the status quo as far as possible is to get an extra data item added to mmCIF for the parameter combination multiplicity*occupancy (I believe this parameter is called the 'site population' in Shel-X).
So in addition to '_atom_site.occupancy' (which is in the core CIF
dictionary) we would have (say) '_atom_site.population' specifically for mmCIF. That way programs that created mmCIF files for deposition could use either parameter without ambiguity, and we don't need to change any existing programs, except for those few that do CIF <-> PDB conversion. Existing macromolecular CIF files would have to be updated to show the new data item, that's all. This assumes of course that that really is the data they actually contain, maybe some don't, that would need to be checked: I suspect the PDB doesn't verify which parameter is actually deposited. Uncertainty about what the 'occupancy' column actually contains in the case of special positions is what we want to resolve. A bit untidy I know, but I can't see any other way that doesn't involve major upheavals.
We would also need to get the PDB Contents Guide changed so that it refers to 'site population' instead of occupancy. That way no programs reading/writing PDB files (except mine!) would need to be changed.
Does anyone have a better suggestion?
-- Ian
On Thu, Dec 16, 2010 at 9:10 PM, Dale Tronrud <[log in to unmask]> wrote:
> On 12/16/10 06:47, Ian Tickle wrote:
>>
>> For the sake of argument let's say that 0.02 Ang is too big to be
>> rounding error. So if you see that big a shift then the intention of
>> the refinement program (or rather the programmer) which allowed such
>> a value to be appear in the output should be that it's real. If the
>> intention of the user was that the atom is actually on axis then the
>> program should not have allowed such a large shift, since it will be
>> interpreted as 'much bigger than rounding error' and therefore
>> 'significantly off-axis'.
>
> I would certainly hope that no one believes that the precision of
> the parameters in a PDB file are significant to the level of round-off
> error! It's bad enough that a small number of people take the three
> decimal points of precision in the PDB file seriously. When a person
> places an atom in a model they aren't stating a believe that that is
> the EXACT location of the atom, only that they believe the center of
> the locus of all equivalent atoms in the crystal falls near that spot.
> If it's 0.02 A from a special position (and the SU of the position is
> larger than that) then it might be on the special position and it
> might not.
>
> If I come across one of your models and you have an atom exactly on
> a special position (assuming you're able to do that with three decimal
> points in a PDB file) I'd still assume that you only intend that there
> is an atom in the vicinity of that point and it might be exactly on
> the axis but it might be a little off. All structural models are fuzzy.
>
> Dale Tronrud
>
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