[phenixbb] Ca occupancy in multiple soaked structures

Pavel Afonine pafonine at lbl.gov
Wed May 22 21:25:46 PDT 2013

Hi Dan,

as few random thoughts:

- I guess this only makes sense to do relatively: say pick one as 1 and 
see the others as fractions of it. Though Fourier maps need to be 
computed using the same sets of Miller indices for comparisons to be 

- Remember you look at Fourier images of electron density, not electron 
density itself... That's the key.

- All in all this means peak heights may mean more than simply site 

- If you go by residual peak parameters (heights, for instance) then it 
doesn't matter how you refined occupancy and B of these Ca, and in which 
ways they are correlated.


On 5/22/13 10:10 AM, Daniel Slade wrote:
> Hi Everyone,
> I have a complex case of data analysis I would love some opinions on.  I have a group of structures of a protein that binds 6 calciums, and we want to know the order/concentration at which they fill.  The crystals were soaked with calcium from 0-10 mM and all are 1.6-2.1 A in resolution.  I determine the order of the calcium binding, and now I am working on the percent occupancy at each concentration.  To do this, I have removed the calciums, and then performed simulated annealing for each structure from 2.1-30A resolution to 'normalize' them.  I then look at the omit map and scroll out to find the peak sigma intensity of where the calciums should be.
> The curves fit very well for each calcium, and the numbers correspond well with other solution studies we have. My thought is that I need to normalize this in another way, so I thought choosing a water molecule that is present in all of the structures and removing it, then performing simulated annealing would be a good idea to normalize the peak intensity for each calcium soak concentration, since this water molecule shouldn't change occupancy.  Is this the proper way to do this, or can you guys suggest a better way to go about this.  I also looked at B factor and e/A3, but that isn't as consistent as peak sigma.
> Thanks in advance.
> Dan

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