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 fit and refine cycle, defaults to 0

-l u,v: only applies to the fit step, will only discretize the given lattice line, not all

-v VERB: verbosity level, default is 3

-d SDIR: adds additional directories containing diffraction data, use one -d parameter per additional dir

COMMAND is one of:

merge

Retrieve the symmetrized dataset (_sym.mtz) from each non-ignored diffraction directory, and merge it together into a single reflection list.

Output: merge0.mtz

scale

Scale each dataset against the merged one.

Input: merge0.mtz

Output: merge_scaled00.mtz

fit

Run the fitting and discretization algorithm for each lattice line.

Input: merge_scaleNN.mtz

Output: merge_llfitNN.mtz merge_discNN.mtz merge_curveNN.mtz

where NN is the cycle number

refine

Refine scaling and/or tilt geometry.

Input: merge_llfitNN.mtz

Output: merge_scaledMM.mtz

where MM is NN+1

all

all of the above, in their logical order merge scale fit refine

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>

  <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>

 <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>

---

Back to Overview