Use case "Indexing with MOSFLM"

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Summary

This use case describes indexing performed by MOSFLM.

Importance Very important
Priority High priority
Use Frequency Frequently used
Direct Actors Kernel / User
Pre-requirements Kernel running

Input

Required

Common data collection parameters:

A list of images:

  • Data collection parameters for each image:
    • Path to image directory
    • Image number
    • Template (containing any eventual run number)
    • Phi start
    • Phi end

Optional

  • Forced symmetry
  • Threshold for using spots in indexing
  • Resolution limit for indexing

Output

Required

  • Orientation matrix
  • Unit cell parameters
  • Possible Space group(s) (Laue group ?)
  • Rms error in spot positions
  • Percentage of spots indexed
  • Shift in main beam position
  • Rms error for the triclinic solution
  • List of all possible solutions
  • Diffraction images with predicted patterns superimposed
  • Parameters to judge success
  • List of warnings / errors

Optional

Main Success Scenario

In EDNA, MOSFLM needs to be started by a shell script for two reasons:

  • When starting a new shell in AALib the environment variables of the father shell are not copied so the CCP4 setup script needs to be loaded.
  • MOSFLM is an interactive program and the most easy way for running MOSFLM non-interactively is by running it in a script.

Here's an example MOSFLM script for indexing two images:

#!/bin/bash
. /opt/pxsoft/ccp4-6.0.2/include/ccp4.setup-bash
/opt/pxsoft/mosflm/v701_20070820/redhate4-i686/bin/ipmosflm-7.0.1-20aug07 DNA edna_mosflm_script.xml > edna_mosflm_script.log 2>&1 << EOF-mosflm
NEWMAT edna_mosflm_script.mat
WAVELENGTH 0.934
DISTANCE 198.4
BEAM 102.5 104.7
DETECTOR adsc
DIRECTORY test-data
TEMPLATE ref-testscale_1_###.img
AUTOINDEX DPS REFINE IMAGE 1 PHI 0.0 1.0
DIRECTORY test-data
TEMPLATE ref-testscale_1_###.img
AUTOINDEX DPS REFINE IMAGE 2 PHI 90.0 91.0
MOSAIC ESTIMATE
GO
EOF-mosflm

Variations

If the success scenarios are not met - what are the conditions for rerunning indexing ? - more images included - symmetry input required

Notes and Questions

Do we have ideas about the accuracy of which we need to know some of the Input parameters - for example - the beam center ? Also, Should we be logging shifts in the beam center ? And then informing the beamline scientist that they need to recalibrate. Often the first sign that something is wrong is that DNA indexing starts failing !