generate r free flags in phenix.refine not obeying high resolution limit?
Hi all When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, it is always the best to generate the free R flags for the whole dataset and this is what phenix.refine does (I will have to double-check, though). Because, for example, if you change your mind and later decide to use more data, you will run into trouble with generating free R flags for the rest of reflections for which you haven't done it in the beginning. Also, phenix.refine generates free R that are evenly distributed over the resolution, making sure that relatively thin resolution bins receive enough of reflections (to assure correct ML estimations). So, I don't see any problem here... Am I missing something? Pavel. On 8/20/2008 8:58 AM, Francis E Reyes wrote:
Hi all
When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ?
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
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Hi Pavel, I'd like to add a question to this. Is there a way in phenix to inherit the test reflections from another reflection file i.e. in .mtz format? thanks Michael Pavel Afonine wrote:
Hi Francis,
it is always the best to generate the free R flags for the whole dataset and this is what phenix.refine does (I will have to double-check, though). Because, for example, if you change your mind and later decide to use more data, you will run into trouble with generating free R flags for the rest of reflections for which you haven't done it in the beginning.
Also, phenix.refine generates free R that are evenly distributed over the resolution, making sure that relatively thin resolution bins receive enough of reflections (to assure correct ML estimations).
So, I don't see any problem here... Am I missing something?
Pavel.
On 8/20/2008 8:58 AM, Francis E Reyes wrote:
Hi all
When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ?
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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Hi Michael, yes - only if you have exactly matching datasets. For example one MTZ (or any other format) file with Fobs and another MTZ (or any other format) file with free-R flags; and the hkl indices in both files are identical. Otherwise, no. I'm not sure, may be Ralf or Peter have some scripts to do this - I remember someone asked for this, but may be I'm wrong... Pavel. On 8/20/2008 9:35 AM, Michael Hothorn wrote:
Hi Pavel,
I'd like to add a question to this. Is there a way in phenix to inherit the test reflections from another reflection file i.e. in .mtz format?
thanks Michael
Pavel Afonine wrote:
Hi Francis,
it is always the best to generate the free R flags for the whole dataset and this is what phenix.refine does (I will have to double-check, though). Because, for example, if you change your mind and later decide to use more data, you will run into trouble with generating free R flags for the rest of reflections for which you haven't done it in the beginning.
Also, phenix.refine generates free R that are evenly distributed over the resolution, making sure that relatively thin resolution bins receive enough of reflections (to assure correct ML estimations).
So, I don't see any problem here... Am I missing something?
Pavel.
On 8/20/2008 8:58 AM, Francis E Reyes wrote:
Hi all
When generating R-Free flags from phenix refine, flags are generated all the way to the limit of the data. However, shouldn't flags be generated up to the limit of the data if specified via refinement.input.xray_data.high_resolutio n ? If not, are the statistics for R/Rfree matching to high resolution data that may be suspicious ?
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
-
Francis E Reyes -
Michael Hothorn -
Pavel Afonine