high resolution bin statistics
Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here: REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
Hi Sebastiano, the number of bins used is such that each bin has enough amount of "free" reflections for meaningful statistics calculation. For example, in your case below only 4 bins allow slightly more than 100 "free" reflections per bin. Making more bins will further reduce the number of "free" reflections per bin making it impossible to compute Rfree in each bin. Pavel. On 8/31/09 3:21 AM, Sebastiano Pasqualato wrote:
Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here:
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890
thanks a lot in advance, ciao s
Thanks Pavel, that sounds more than reasonable! have a nice day, ciao s On Aug 31, 2009, at 5:55 PM, Pavel Afonine wrote:
Hi Sebastiano,
the number of bins used is such that each bin has enough amount of "free" reflections for meaningful statistics calculation. For example, in your case below only 4 bins allow slightly more than 100 "free" reflections per bin. Making more bins will further reduce the number of "free" reflections per bin making it impossible to compute Rfree in each bin.
Pavel.
On 8/31/09 3:21 AM, Sebastiano Pasqualato wrote:
Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here:
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890
thanks a lot in advance, ciao s
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-- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094
participants (2)
-
Pavel Afonine -
Sebastiano Pasqualato