[phenixbb] missing map coefficients

Anne Mølgaard anne at kemi.ku.dk
Thu Jan 15 12:48:05 PST 2009


Hi Tom,

Thanks for your help! 

Best regards,

Anne

"Tom Terwilliger" <terwilliger at lanl.gov> skrev:
> 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
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
> 
> 

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