Nate, the common wisdom seems to be that setting aside 1000-2000 reflections is enough to ensure proper statistics anything more is overkill. I am not sure about the exact reference for these numbers, but you could start with Axel Brunger's original paper about refinement with FreeR. Also a couple of Ian Tickles latest papers deal with the issue. HTH Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Nate Nicely Sent: Tuesday, January 19, 2010 12:29 PM To: [email protected] Subject: [phenixbb] Reflection file conversion
I use d*TREK to reduce my data and phenix.reflection_file_converter to import the data. I seem to have had a bit of trouble generating the free R flags. It seems that the cap for the max number of free R reflections takes precedence over the percentage, even when the percentage is given expressly on the command line. I find myself setting the cap artificially high on the command line so that a full 10% is set aside.
I was taught to set aside 10% for the free R set, only going lower if setting aside the full 10% compromised completeness. I'm just wondering what is the rationale for the numeric cap? Am I making any error(s) with my methodology?
Nate N
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