[phenixbb] scaling in Fo-Fo maps

Smith Liu smith_liu123 at 163.com
Thu Feb 4 09:50:15 PST 2016

Hi Pavel,
In line with the question of Xun, will you please introduce a way to scale-up the intensity of cryo-EM to the level of intensity of x-ray crystallography? I have a read a paper, in which the author have done the above-mentioned scaling-up in order to use the phenix reciprocal space  refine for cryo-EM data refine, but the paper method was very difficult to  understand. Currently with the availability of pheinix.real_space_refine, in a lot of situations reciprocal refine for cryo-EM data is still necessary.

At 2016-02-05 00:51:18, "Pavel Afonine" <pafonine at lbl.gov> wrote:
>Hi Xun,
>> I have a question on how the scaling is done when generating Fo-Fo 
>> maps in Phenix.
>I read you are asking about scaling in Isomorphous Difference Map 
>(Phenix GUI -> Maps) or its command line equivalent 
>When implementing Fo-Fo map calculation in Phenix I could not find 
>literature that would sufficiently describe the protocol so I could use 
>it to write code (which is very typical for crystallographic protocols 
>and algorithms, unfortunately!). So I had to "re-invent the wheel" 
>myself from scratch. Below is the protocol I came up with.
>Looking at the code in /cctbx_project/mmtbx/maps/fobs_minus_fobs_map.py:
>You input two sets of Fobs: Fo1 and Fo2 and PDB file with a model that 
>serves as a source of phases. It's your responsibility to prepare this 
>model appropriately.
>Then common sets are obtained: Fo1, Fo2 = Fo1.common_sets(Fo2) . This is 
>because Fo1 and Fo2 arrays may have different not necessarily matching 
>Miller indices hkl.
>The following is then done:
>Fmodel1 = ktotal1 * (Fcalc + Fbulk1)
>Fmodel2 = ktotal1 * (Fcalc + Fbulk2)
>are obtained from fitting to Fo1 and Fo2, correspondingly.
>Then normalized Fobs are obtained (on "absolute" scale): Fo1n = 
>Fo1/ktotal1 and Fo2n = Fo2/ktotal2
>Then they are scaled to each other using one scalar scale factor:
>k = SUM(Fo1n*Fo2n) / SUM(Fo2n**2)
>Instead (optionally), they can be scaled to each other using 
>"multiscale" protocol, very similar to what used to be in CNS, if you 
>know what I mean.
>Finally, the synthesis is computed as {Fo1n - k*Fo2n, phases from one of 
>Fmodel above}. I can't see in the code which one of the two Fmodels I 
>choose, I think it's arbitrary.
>> But I also want to compare the peaks in the three maps, so I want to 
>> make sure the maps are generated using the same scaling.
>See other email posted to phenixbb from Sacha Urzhumtsev. This is the 
>way to do it! It is implemented in Phenix GUI: Maps->Map Comparison.
>More intuitively, the procedure is described in Section "2.9. Note about 
>the comparison of maps" here:
>FEM: feature-enhanced map. P.V. Afonine, N.W. Moriarty, M. Mustyakimov, 
>O.V. Sobolev, T.C. Terwilliger, D. Turk, A. Urzhumtsev, and P.D. Adams. 
>Acta Cryst. D71, 646-666 (2015).
>Hope this answers your questions!
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