[phenixbb] cut out density vs FFT

Pavel Afonine pafonine at lbl.gov
Tue Feb 19 11:22:49 PST 2013

Hi Yunji,

you can try


which is an alternative implementation of the idea of extracting a model 
and a map in a box around selected atoms. Since I wrote it I know for 
the matter of fact that it does what I just wrote above: extracts model 
and map in a box around selected atoms, and nothing else.

An example of using it:

phenix.map_box model.pdb map_coefficients.mtz selection="chain A and 
resseq 1:10" label='2FOFCWT_no_fill'

and it will output 4 files:

one PDB file with selected atoms in the box, one MTZ file with map 
coefficients and two actual map files in CCP4 and X-plor formats, so you 
have choices which one is more convenient for you to use.

Let me know if you have questions.


On 2/19/13 11:06 AM, Yunji Wu wrote:
> Hi all--
> I'm trying to make a 2Fo-Fc map with density wrapped around my asymmetric unit to make a figure showing density for my sub-8Å structure. I am not building into this map or doing MR. My model was refined in Phenix.refine (R's in the high 30's), and so I have the output model .pdb and the output map coefficients .mtz. When I input these into cut_out_density, the only "map labels" input options it gives me are 2FOFCWT, PH2FOFCWT, which seem fine. Using either box, sphere, or model for the cutout type, I get a VERY nice looking map that looks extremely solvent flattened and tight around my model, albeit still to 8Å.
> Suspicious of anything that looks good, I went to try the same thing in FFT (CCP4). There I generated a simple map (using the same .mtz) to cover all atoms in a pdb file- the same model I put into cut_out_density. For the input I selected 2FOFCWT and PH2FOFCWT, leaving Sigma and Weight unassigned. The map that comes out of this looks terrible, with a lot of noise and little density corresponding to the model aside from what one might expect from a very poor resolution experimental map. I've also tried using FFT in Phenix to do the same thing, and it gives like better maps than CCP4 FFT but worse than cut_out_density. It almost appears as if there is some additional solvent flattening going on, which I know happens at the beginning of refinement, but that should be intrinsic to the map coefficients file which is common to everything I've tried.
> My questions are (1) what should I use for what I am trying to do (just display 2Fo-Fc density around asymmetric unit for a figure) and (2) what is the difference between what these three programs (cut_out, FFT-CCP4, FFT-Phenix) are calculating? The inputs are exactly the same -- mtz (2FOFCWT and PH2FOFCWT) and pdb output from refinement.
> Thanks for the help,
> Yunji
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