[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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