missing map coefficients
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
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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Hi Tom,
Thanks for your help!
Best regards,
Anne
"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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participants (2)
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Anne Mølgaard -
Tom Terwilliger