Increasing negative values of the relative B factor are an indicator of deterioration with dose, although the B factor is also affected by factors other than radiation damage. A negative SD value indicates no tie. Analysis of various parameters as a function of batch or image number, a proxy for crystal rotation, time or radiation dose, is useful to determine whether the crystal has suffered unduly from radiation damage or whether there are any other parts of the data which should be discarded. The scale factor is a function of the primary beam direction, either as a smooth function of Phi the rotation angle ROT , or expressed as BATCH image number strongly deprecated. The main problem is that we have become accustomed to using the nominal resolution as an indicator of model quality, and it is not a good indicator, particularly as important biological and chemical conclusions from a structure often depend on local rather than global correctness. Unfortunately, this has been hard to prove:
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Each observation is assigned to a “run”, which corresponds to a set of scale factors.
Note that it will always increase significantly in the high-resolution shells. The two or three orthogonal principal directions of anisotropy are simless by the lattice symmetry: Define rejection criteria for outliers: By comparing refinement against measured data with refinement against simulated data, we can judge the resolution point at which the measured data become no better than simulated data and compare this with the data-processing statistics.
Running the program Scaling options Control of flow through the program Partially recorded reflections Scaling algorithm Data from Denzo Datasets. By default, the datasets with the shortest wavelength will be chosen aim,ess the base or dataset 1 if wavelength is unknown.
Only do the merge step, no initial analysis, no scaling. Partials may either be summed or scaled: Acta Crystallogr D Biol Crystallogr. Their use as it relates to unmerged data is described below.
How good are my data and what is the resolution?
A note on terminology: Here, we analyse the effect of the procedure used to estimate the amplitude F from the measured intensity I when data are very noisy. The default is to use a weighted mean, depending on the “raw” intensity ie before LP correction COMBINE optionand to optimise automatically the switch-over point Imid, to give the best overallR meas.
For each run, a relative B-factor Bi is determined at intervals in “time” “time” is normally defined as rotation angle if no independent time value is availableat positions ti t1, t2. Similar results were obtained with example 4, omitting the last domain residues: Under the assumption that true structure factors come from a crystal filled with atoms randomly distributed over the unit cell and the noise in the experimental intensities has a normal distribution, the TRUNCATE procedure estimates the amplitudes of structure factors using a Bayesian estimation with the formula.
There are several workarounds possible: Apply or remove restraints to parameters.
Analyzing unmerged data in Phenix
The effect of resolution on the visual appearance of difference maps was tested on regions of the model which were not included in refinement. Obviously, the behaviour of this statistic depends on the statistical properties of the structure factors. Set which intensity to use, of the integrated intensity column I or profile-fitted column IPRif both are present. We recommend that you use the unmerged data if available, as they are more reliably parsed than logfiles.
Problems with new PDF generator fixed in snapshot release The snapshot release introduced the zimless PDF report generator feature. By default, the datasets with the shortest wavelength will be chosen as the base or dataset 1 if wavelength is unknown. Then for an observation measured at time tl.
Dump all scale factors to a file after the main scaling.
When running on single-sweep datasets and without using the -d flag, there could be an error message. The procedure differs between various data-processing software; these are the methods we are familiar with:.
For this, a two-stage procedure is used: For each reflection h, we have a number of observations Ihl, with estimated standard deviation shl, which defines a weight whl. A negative SD value indicates no tie. Similar tests were carried out for examples 4 and 5 see Figs.
D 59— If no RUN command is given then run assignment will be done automatically, with run breaks at discontinuities in dataset, batch number or Phi.