[phenixbb] density level

[Pavel Afonine]

Hi,

what kind of file you use to see the map in Coot: Fourier map 
coefficients (MTZ file) or actual map (CCP4 binary formatted file with 
the map)? I need to know this before offering a first guess on what may 
be the reason for this.

Pavel

On 1/13/13 11:38 AM, CPMAS Chen wrote:
> Dear PhenixBBer,
>
> I recently updated my old phenix-1.6.4-486 to phenix-dev-1266. To 
> my surprise, the absolute electron density on the 2Fo-Fc map is quite 
> different.
>
> https://www.dropbox.com/s/prs0z8ayb73kg9k/Screenshot_sigma.png
>
> At the same sigma level(1.5), the absolute density of the violet map 
> is 0.32e/A^3 (phenix-dev-1266), while that of the blue map is 
> 0.01e/A^3(phenix-1.6.4-486). Besides the different phenix used, there 
> is no other difference on the data and model used.
>
> Sam encountered a similar problem on the density.
>
> http://phenix-online.org/pipermail/phenixbb/2012-December/019226.html
>
> By the way, is there a simple way to keep only F and SIGF column of 
> the autoxds generated truncate.mtz via phenix? the GUI does not allow 
> to reduce columns. I normally use IMEAN and SIGIMEAN to do refinement, 
> but this may not be necessary as it is pointed in the maillist, since 
> the intensity is already transformed to amplitude after truncation in 
> autoxds.
>
> I can specify labels by xray_data.labels = "F, SIGF", but apparently 
> phenix treats it as containing anomalous data. the following is 
> extracted from the refine pdb file
>
> MIN(FOBS/SIGMA_FOBS)              : 1.16
> REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.11
> REMARK   3   NUMBER OF REFLECTIONS             : 143207
> REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 73247
>
> Also, in the auto generated def file,
> xray_data.labels = "F, SIGF, DANO, SIGDANO"
>
> Or there is a work round for this issue?
>
> Thanks!
>
> -- 
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
>
>
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