[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right? i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0". -bryan (some error output below) Sorry: R-free flags not compatible with F-obs array: missing flag for 22206 F-obs selected for refinement:
[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ]
if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right?
I think that's true. Nat wrote a more comprehensive tool for generating R-free flags, which are included in recent nightly builds. I'm pretty sure Nat generates the flags for all possible reflections.
i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0".
Hm... not sure I understand, but try Nat's new tools first. It is easiest through the GUI, but there's also a command-line version, phenix.reflection_file_editor. Ralf
On Nov 13, 2009, at 1:18 PM, Bryan W. Lepore wrote:
On Fri, 13 Nov 2009, Ralf W. Grosse-Kunstleve wrote:
[..] there's also a command-line version, phenix.reflection_file_editor.
thanks -- this seems to launch the gui - suppose i need to get the nightly?
1.5-2 should work for most things - but the newer builds make it much easier to edit individual labels and manipulate data, and can assign R- free flags in thin resolution shells. I don't think any of this will help in your case, however (unless I completely misunderstood the question). ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
On Nov 13, 2009, at 1:08 PM, Ralf W. Grosse-Kunstleve wrote:
[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ]
if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right?
I think that's true. Nat wrote a more comprehensive tool for generating R-free flags, which are included in recent nightly builds. I'm pretty sure Nat generates the flags for all possible reflections.
i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0".
Hm... not sure I understand, but try Nat's new tools first. It is easiest through the GUI, but there's also a command-line version, phenix.reflection_file_editor.
I'm not sure I understand either - does this mean that the MTZ file with the test set only has Miller indices (i.e. h,k,l) for the reflections actually in the test set, and the work set is simply missing? If so, I'm almost certain that my program isn't going to do any better, since it assumes that the R-free flags are comprehensive, but if you send me (not the list!) the reflection files I can probably fix them quickly. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (3)
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Bryan W. Lepore -
Nathaniel Echols -
Ralf W. Grosse-Kunstleve