[phenixbb] missing map coefficients

[Tom Terwilliger]

Hi Anne,

I'm sorry for the unclear labelling in that file.   FP is 2FOFCWT and  
PHIM is PH2FOFCWT.  I will try to make this more clear, and later, to  
use the right labels.

If you really want the original mtz file from phenix.refine with these  
coefficients, and the FOFCWT and PHFOFCWT coefficients, you can look  
in the TEMP0/ subdirectory, and find a file with a name like:

refine_map_coeffs_3.mtz

which will be the refinement map coefficients from refinement #3 .  
Look in the log file for something like:

New overall best saved:

Current overall_best model and map  Thu Jan 15 07:14:48 2009
Working directory: /net/chevy/raid1/terwill/misc/test/AutoBuild_run_20_
Model (overall_best.pdb) from: Build_composite_refined_3.pdb

and that refined_3 goes with map_coeffs_3.

I hope that helps!
-Tom T




On Jan 15, 2009, at 3:20 AM, Anne Mølgaard wrote:

> I am new to Phenix, so there might be an easy explanation for this  
> problem, though I have not been able to find a solution in the  
> documentation. I am using phenix version 1.3b-rc4, intel-linux-2.6.
>
> I have solved a structure using phenix.automr, followed by  
> phenix.autobuild (run from command line using "phenix.autobuild  
> data=fromXDS_unique.mtz model=AutoMR_run_2_/MR.1.pdb  
> seq_file=sequence.fas"). The program runs succesfully, and I get the  
> output files I should expect. However, the  
> overall_best_refine_map_coeffs.mtz does not contain the map  
> coefficients 2FOFCWT PH2FOFCWT for the 2mFo-DFc map and FOFC and  
> PHFOFC for the Fo-Fc difference map. mtzdmp gives me the following  
> columns:
>
>    1 ASC      0      28      0  100.00     10.6     10.6  28.28    
> 1.85   H  H
>    2 NONE     0      35      0  100.00     13.3     13.3  28.28    
> 1.85   H  K
>    3 NONE     0      71      0  100.00     26.6     26.6  28.28    
> 1.85   H  L
>    4 NONE    1.0  1888.8     0  100.00   148.71   148.71  28.28    
> 1.85   F  FP
>    5 BOTH    1.0     1.0     0  100.00     1.00     1.00  28.28    
> 1.85   Q  SIGFP
>    6 NONE -180.0   180.0     0  100.00     2.08    90.23  28.28    
> 1.85   P  PHIM
>    7 BOTH  1.000   1.000     0  100.00    1.000    1.000  28.28    
> 1.85   W  FOMM
>    8 NONE     .0    19.0     0  100.00     9.50     9.50  28.28    
> 1.85   I  FreeR_flag
>    9 BOTH     .0      .0     0  100.00      .00      .00  28.28    
> 1.85   F  FC
>
> What should I do to get these map coefficients?
>
> Thanks for your help!
>
> Best regards,
>
> Anne
>
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> phenixbb at phenix-online.org
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