Hi, is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does. I tried with phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz --low-resolution=2.6 --resolution=2.5 but with the default settings, phenix.refine writes 2FOFCWT and FOFCWT, but not FC . So it looks like I have to re-run phenix.refine and make it write out FC? Or is it easier to run phenix.xmanip for that purpose? thanks, Kay
On Wed, Aug 4, 2010 at 10:22 AM, Kay Diederichs < [email protected]> wrote:
is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does.
phenix.refine will print R-factors by resolution shell, but the number of shells it decides to use varies with the number of reflections - for a really small structure (e.g. amyloid peptide) you will have only one resolution shell (the argument being that R-free statistics aren't reliable if you have very few reflections in the test set). You can set an upper limit on this (refinement.main.max_number_of_resolution_bins), but it won't give you ten shells if phenix.refine wants to use, say, five. There may be another way to get this information that I'm not aware of, but I've always done it directly in Python. I've been working on a project that potentially requires changing phenix.model_vs_data to report these statistics; my plan was to use the last of ten shells, since both HKL2000 and SCALA report everything that way (don't know about XDS since I haven't used it). Is this sensible, or does it need to be more flexible and accept explicit resolution ranges? (I'm not actually sure whether this is possible right now, but 10 shells is easy.) -Nat
Hi Kay, 0) I guess by FC you actually mean Fmodel, see page #6 here http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p... 1) you can ask phenix.refine to output Fcalc, Fmodel, Fbulk, FOM, alpha, beta, TestFlags, Fobs etc... Example that does just this (after bulk solvent correction and anisotropic scaling): phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 export_final_f_model=mtz or phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 export_final_f_model=mtz 2) I will add detailed R-factor statistics output as part of phenix.model_vs_data tool. 3) phenix.refine chooses the amount of resolution bins based on availability of free-R flags (so each relatively thin resolution shell receives not less then ~150 test reflections). By the way, "150" or so is the parameter that you can change. Apart from cosmetics (the amount of output bins) this will influence the refinement too. Let me know what exactly you are trying to achieve and I will think how we can accommodate it in available tools. Pavel. On 8/4/10 10:22 AM, Kay Diederichs wrote:
Hi,
is there a way to get the R-factor statistics from phenix.refine, for a specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would like to specify the same resolution range as the data reduction program does.
I tried with phenix.reflection_statistics x_map_coeffs.mtz x_data.mtz --low-resolution=2.6 --resolution=2.5
but with the default settings, phenix.refine writes 2FOFCWT and FOFCWT, but not FC . So it looks like I have to re-run phenix.refine and make it write out FC? Or is it easier to run phenix.xmanip for that purpose?
thanks,
Kay
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participants (3)
-
Kay Diederichs -
Nathaniel Echols -
Pavel Afonine