iplt_diff_merge

Syntax

iplt_diff_merge COMMAND [-w DIR] [-c CYCLE] [-l POINT] [-v VERB] [-d SDIR1 [-d SDIR2]]

Iterate over all image directories in the current dir, plus all directories added with the -d option, and perform one of the commands for merging (see below). The parameters are:

-w DIR: store merging results in DIR (defaults to ./merge). An info.xml file in this directory will be imported and overrides parameters from project.xml.

-c CYCLE: choose refinement cycle, defaults to 0

-v VERB: verbosity level, default is 3

COMMAND is one of:

scale

Scale each data set against the merged one. The merged data set is created on the fly.

Output: merge_mergedNN.mtz merge_scaledNN.mtz

where NN is the cycle number

tgrefine

Refine scaling and/or tilt geometry.

Input: merge_scaledNN.mtz

Output: merge_tgrefNN.mtz

where NN is the cycle number

llfit

Run the fitting and discretization algorithm for each lattice line.

Input: merge_tgrefNN.mtz

Output: merge_llfitNN.mtz merge_discNN.mtz merge_curveNN.mtz

where NN is the cycle number

all

all of the above, in their logical order scale tgrefine llfit

xml parameters

The following xml tags are recognized in the project.xml file, or in an info.xml file in the merge destination dir

<Scale>
  <!-- resolution limits -->
  <Resolution>
    <low value="40" type="float"/>
    <high value="2.5" type="float"/>
  </Resolution>
  <!-- number of bins for the weighted bin scaling -->
  <BinCount value="16" type="int"/>
  <!-- cutoffs for the filtering step after scaling, based on the weighted bins -->
  <WBinISigICutoff value="0.1" type="float"/>
  <WBinSigmaCutoff value="10.0" type="float"/>
  <!-- minimum tilt angle (in degree) for which to invoke an anisotropic pre-scaling-->
  <AnisoMinTilt value="90" type="float"/>
</Scale>

<Refine>
   <!-- lattice line curve fitting mode 0 (based on Imax and z*max) or 1 (bases on sigmaI and sigmaz*) -->
   <CurveFitMode value="0" type="int"/>
   <!-- zstar fudge factor, experimental -->
   <ZWeight value="8.0" type="float"/>
   <!-- flag to turn intensity scale refinement on or off -->
   <RefineScale value="1" type="bool"/>
   <!-- flag to turn tilt geometry refinement on or off -->
   <RefineTilt value="1" type="bool"/>
   <!-- resolution limits to determine new tilt geometry -->
   <RefineTiltRLow value="10" type="float"/>
   <RefineTiltRHigh value="4" type="float"/>
 </Refine>

<LLFit>
  <!-- experimental weighting algorithms, use mode 1 and cutoff 0.0 for all practical purposes -->
  <Weighting>
    <T1 value="10.0" type="float"/>
    <T2 value="40.0" type="float"/>
    <Mode value="1" type="int"/>
    <Cutoff value="0.0" type="float"/>
  </Weighting>
  <!-- iteration limit for the internal non-linear fitting routine -->
  <MaxIterations value="1000" type="int"/>
  <!-- iteration precision for the internal non-linear fitting routine -->
  <IterationPrecision value="1e-2" type="float"/>
  <!-- bootstrapping mode for improved sigma generation, recommended -->
  <BootstrapFlag value="1" type="bool"/>
  <BootstrapIterations value="20" type="int"/>
  <!-- initial guess mode prior to fitting; 0=from weighted bins, 1=random phase, unit amplitude, 2=totally random-->
  <GuessMode value="0" type="int"/>
  <!-- multiple iterations with different starting values, not as powerful as bootstrapping, best kept at 1 -->
  <Iterations value="1" type="int"/>
  <!-- phantom mode includes two additional values at +- sigma z* -->
  <PhantomMode value="0" type="bool"/>
</LLFit>