[phenixbb] Partially reduced disulfides

Pavel Afonine pafonine at lbl.gov
Thu Mar 22 20:35:34 PDT 2012

Hi Chris,

it's a bit difficult for me to follow your description without actually 
looking at the structure...
Could you send me the PDB file and tell occupancies of which atoms 
should be refined and how, then I will try to suggest how to instruct 
phenix.refine to do what you want.


On 3/22/12 7:33 PM, Christopher Wanty wrote:
> Hi,
> I have a structure that appears to have a combination of reduced and 
> oxidised disulfides.
> From previous reading on the board I've taken the strategy of dropping 
> the disulfide detection cutoff to 0.1 then added back the disulfides 
> as appropriate using restraints. The problem I now have is that for 
> some of these cysteine pairs there are clearly oxidised and reduced 
> positions in the density. Modelling altloc's for each of these works, 
> but the occupancies do not refine as I expected; the altloc's involved 
> in the disulfide I expected to have the same occupancy as their 
> counterpart in the disulfide.
> To try to get these to match, I introduced occupancy constraint that 
> look like:
> constrained_group {
>         selection = (chain A and resseq 276 and altloc B) or (chain A 
> and resseq 286 and altloc B)
>       }
> But with that the sum of occupancies for altloc 276 (for example) is 
> not adding to 1.00. My thought is that I need to change the occupancy 
> constraints but I'm not sure how to make them do what I want.
> Any help/advice is appreciated.
> Regards,
> Chris
> -------------------------------------------------------
> Dr. Christopher Wanty
> christopher.wanty at uwa.edu.au
> Research Associate
> Biomolecular, Biomedical and Chemical Sciences,
> Building M310
> University of Western Australia
> 35 Stirling Highway
> Crawley 6009
> Western Australia
> Australia
> _______________________________________________
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