Requested mtz.dump inserted later in letter. Pavel Afonine wrote:
Hi Dale,
1) Why you specify reflection MTZ file twice in phenix.refine script?
I put the mtz in twice because if I put it in once phenix.refine complains that I have no free R flags. It seems to want one file with the amplitudes and another with the flags. Since I have both in the same file I put that file on the line twice and phenix.refine finds everything it needs.
phenix.refine looks for free-R flags in your main data file (1M50-2.mtz). Optionally you can provide a separate file containing free-R flags (I have to write about this in the manual). However, if your 1M50-2.mtz contains free-R flags then you don't need to give it twice. So clearly something is wrong at this step and we need to find out what is wrong before doing anything else. Could you send the result of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your data file? Or I can debug it myself if you send me the data and model.
dale@fluorine [2] phenix.mtz.dump 1M50-2.mtz Processing: 1M50-2.mtz Title: [No title given] Space group symbol from file: P 43 3 2 Space group number from file: 212 Space group from matrices: P 43 3 2 (No. 212) Point group symbol from file: PG432 Number of crystals: 2 Number of Miller indices: 45448 Resolution range: 119.572 2.14861 History: From FREERFLAG 8/12/2007 00:31:08 with fraction 0.050 From f2mtz 8/12/2007 00:31:02 data from CAD on 8/12/07 Crystal 1: Name: HKL_base Project: HKL_base Id: 1 Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 4 label #valid %valid min max type H 45448 100.00% 0.00 45.00 H: index h,k,l K 45448 100.00% 1.00 78.00 H: index h,k,l L 45448 100.00% 0.00 55.00 H: index h,k,l FreeR_flag 45448 100.00% 0.00 19.00 I: integer Crystal 2: Name: allen-2002 Project: FMO-ct Id: 2 Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: 1 Id: 1 Wavelength: 0 Number of columns: 2 label #valid %valid min max type FP 41607 91.55% 0.00 15171.00 F: amplitude SIGFP 41607 91.55% 0.00 1716.00 Q: standard deviation
If the MD5 hash of the test set depends on the resolution then certainly I could be in trouble.
No. It must always use the original files before any processing.
Does the resolution limit affect the MD5 hash of the test set?
No. If it does then it is a very bad bug. I will play with this myself later tonight.
3) Does this work:
(...) I'll try these but it will take a bit of time.
Don't run it until completion. Just make sure it passed through the processing step.
Pavel.
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