[cctbxbb] solvent mask

Peter Zwart PHZwart at lbl.gov
Wed Oct 17 22:00:06 PDT 2007


Hi Celine,

This is relatively straightforward with the sfcalc jiffy from 
$mmtbx/mmtbx/examples/sfcalc.py

and should serve as a good example if you want to recode this yourself.

HTH

Peter








Ralf W. Grosse-Kunstleve wrote:
> Hi Celine,
>
>   
>> Thank you for all those explanation. In fact the problem for me is not
>> the mean of the recalculated map obtained but the range of it, which is
>> no longer one.
>>     
>
> Did you consider using the raw mask with the ones and zeros directly?
> That's the .data attribute of the bulk_solvent object. It is an
> integer array, but you can convert it with .data.as_double().
> See also the .mask_as_xplor_map() method.
>
> The only thing the FFT back and forth does is to introduce
> the Ewald-sphere truncation, which leads to a smoothing of the
> original mask. If you want that, a quick-and-dirty approach is
> to copy the .structure_factors() method, rename it, then replace
> miller_set.unit_cell().volume() with 1.0 in the computation of scale.
> I think you still need to divide by the number of grid points.
> Use the .fft_map() of the structure factors object (miller.array)
> returned by your modified method to get back a map with truncation
> effects, but on the same scale is the original mask.
>
>   
>> To be more clear, what I am trying to do is to "calculate" data at
>> different solvent contrasts from a pdb file. So I have a series of
>> solvent electron densities and I would like to use the complex formula F
>> = Fprotein in vacuum + solvent density*Fmask where Fmask are the
>> structure factors from an indicator function that is 1 in the solvent
>> region and 0 in the protein region (= my cctbx mask).
>>     
>
> That sounds exactly like what's done by the f_model class, which will
> refine the "solvent density" for you. I think you can also specify
> a value. See mmtbx/mmtbx/examples/f_model_manager.py and the
> Computing Commission Newsletter No. 5
> (http://cci.lbl.gov/publications/download/iucrcompcomm_jan2005.pdf).
> The code in the newsletter article is out of date, but the math
> is still accurate and examples/f_model_manager.py is the updated
> code.
> Fcalc in the newsletter formula (page 10 of the .pdf document)
> is your "Fprotein in vacuum". ksol is your "solvent density".
> You can set Uaniso and Bsol to 0 if you want.
>
> Ralf
>
>
>
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>   


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