mosflm Help Routines







































































































REFINEMENT


usage:   The transformation between predicted reflection positions and their


   observed positions (centroids) in the digitised image is refined for
  each image separately. The refined parameters are the camera
  constants, and "distortion" parameters: crystal to detector distance
  (XTOFRA), detector Y axis scale factor (YSCAL), tilt and twist of the
  detector. In addition for detectors that perform a spiral scan (Mar
  Research, DIP and Mac Science) a radial offset (ROFF) and a tangential
  offset (TOFF) are refined (these allow for mechanical misalignment
  in the detector). There is the option to refine radially dependent
  offsets RDROFF and RDTOFF, but by default these parameters are NOT
  refined. All these parameters may be assigned initial values with
  the CAMCON and DISTORTION keywords. The refinement is initially
  performed using strong reflections from the centre of the image, and
  then goes on to use reflections over the entire image.


  The contribution of each selected spot to the positional refinement
  is weighted by the estimated error in its centroid position (based
  on counting statistics). Thus strong spots will get a higher weight
  than weak ones. The refinement (by default) minimises the weighted
  residual. Both the weighted and unweighted residuals are printed in
  the output. The weighted residual should always be close to unity
  irrespective of the strength of the image or size of the spots. The
  unweighted residual will be greater for weak images or large spot
  sizes.


      The selection of reflections, which parameters are refined and
  some aspects of the refinement are controlled by the following
  keywords:







FIX



usage:   This allows individual parameters to be kept fixed during the


   positional refinement. Any of the following parameters may be fixed:
  XCEN, YCEN, CCOMEGA, YSCALE, XTOFRA, TILT, TWIST, ROFF, TOFF, RDTOFF,
  RDROFF.

  eg REFINEMENT FIX ROFF TOFF


  will prevent refinement of parameters ROFF, TOFF (radial and
  tangential offsets).
  For very weak images, it may be best to fix ROFF and TOFF for images
  collected on Mar, DIP or Mac Science detectors.


  
Default: For Mar, DIP and Mac Science scanners all parameters listed
  above are refined with the exception of RDROFF and RDTOFF, which
  must be explicitly turned on with a REFINEMENT FREE keyword. The
  radially dependent distortion parameters are only refined when using
  data from the entire image.
  For all other detectors, ROFF,TOFF, RDROFF, RDTOFF are not
  appropriate and are not refined.







FREE



usage:   This allows parameters that are normally fixed to be refined. The


   only parameters in this class are the radially dependent radial and
  tangential offsets (RDROFF and RDTOFF). These parameters should only
  be refined when working with strong high resolution images. They
  will not normally make any detectable difference to the processing,
  unless there is a problem with the alignment of the detector optics.

  eg REFINEMENT FREE RDTOFF











NREF

usage:   NREF <MINREF>


   Sets the minimum number of reflections for refinement of the
    detector parameters using data from the central region of the
    detector. If fewer than this number are found, the program will
    abort. When processing data from small moleclues it may be
    necessary to reduce MINREF from its default value of 20.
    
Default: 20







NOWEIGHT



usage:   Minimise the unweighted residual rather than the weighted one.


 

  
Default: Minimise the weighted residual









REJECTION

usage:   


   REJECTION <REFREJ> 


  Controls rejection of individual reflections from refinement. If the
  difference between calculated and observed positions is more than
  REFREJ*(estimated error in centroid position) the reflection is
  rejected.


  
Default: 3.0







NSIG



usage:      NSIG <ISIG>


 

  When refining using reflections from the central region of the image
  (CENTRS), those reflections with an observed standard deviation in
  the pixel values less than ISIG times a calculated standard
  deviation based on counting statistics are rejected as too weak (see
  description of CENTRS).  This type of comparison is used rather than
  a test on integrated intensity because the measuring box is not used
  when refining the central region (unless USEBOX is specified), so as
  to give a larger radius of convergence.  If the spots are small
  compared to the size of the measurement box it may be necessary to
  change the default value.  


  DEFAULT: 6 but this is reduced automatically if too few spots found.







INCLUDE



usage:   INCLUDE [PARTIALS <PTMIN> OVERLOADS]


 

  This keyword controls selection of reflections for positional
  refinement, both in the central region of the image (CENTRS) and the
  outer region (SEEKRS or NEXT). Normally only fully recorded,
  non-overloaded reflections are allowed, unless there are relatively
  few fully recorded reflections (see the FULLFRAC subkeyword) in
  which case partials are automatically included.


  The automatic inclusion of partials can be overridden by using the
  INCLUDE subkeyword (and the FULLFRAC subkeyword) with the
  appropriate subkeyword.


  Partials will be selected only if their degree of partiality is
  greater than <PTMIN> (defaults to 0.8 but can be changed by giving
  an appropriate value after the subkeyword PARTIALS:



  eg REFINEMENT INCLUDE PARTIALS 0.5 


  will include any partial more than 50% recorded)


  The program will now automatically reduce PTMIN




  Overloads are ALWAYS excluded from the average spot profile.


  ***** IMPORTANT ****


  If partials are used for positional refinement, then by default
  partials will ALSO be included when forming the standard profiles
  for integration. If you do not want this to happen, include the
  keywords: PROFILE FULLS


  
Default: Partials are not used unless the fraction of fully recorded
  reflections is less than that specified by the FULLFRAC subkeyword,
  or the program cannot find enough fully recorded reflections for
  positional refinement, in which case partials are automatically
  included.







FULLFRAC



usage:   FULLFRAC <frac>


 

  This governs whether partially recorded reflections are included in
  refinement of the detector parameters (see also INCLUDE subkeyword for
  more details). For the FIRST image to be processed, if the fraction of
  reflections generated on that image that are fully recorded is less than
  "frac", then partials are automatically included. 


  Unless the PROFILE FULL keywords are given, this will also mean that
  partials will be included in formation of the standard profiles. Note that
  ONLY the first image is used when setting the decision on whether or not
  to include partials.


  Default value for "frac": 0.333







LIMIT



usage:      LIMIT <x>


 

  When refining the detector and distortion parameters using
  reflections from the central region of the image (CENTRS), only
  reflections with X and Y  coordinates less than "x" mm are
  used.  


  DEFAULT Depends on detector.









RESIDUAL

usage:      RESIDUAL <x>


 

  Sets the maximum allowed final residual in  CENTRS  (ie  for
  central region of the image) or in SEEKRS (ie refinement over
  the whole image) if processing is to  continue.  


  DEFAULT 5.0







CYCLES

usage:      CYCLES <NCYCLES>


   Sets the number of refinement cyles in CENTRS.  For  problem
  images,  eg when spots are very close along the rotation axis
  it can be beneficial to increase NCYCLES.


  DEFAULT 2









IMIN



usage:    IMIN <SDFMIN [SDFINC]>


 

  Controls selection of refinement spots in the outer regions of the
  image (SEEKRS). Reflections with an integrated intensity greater
  than SDF_BIN*(SIGMA(I)) will be selected, where SIGMA(I) is
  calculated from counting statistics.  SDF_BIN is set to SDFMIN in
  the outermost regions of the image and incremented by SDFINC for
  each bin working towards the centre.  If only SDFMIN is given,
  SDFINC defaults to SDFMIN/2 


  
Default: 40, 10, but these values are automatically reduced by
  program if too few spots found.







BGREJ



usage:    BGREJ <BGFREJ>


 

  Spots in which more than a fraction BGFREJ of the background pixels
  have been rejected as outliers from the background plane will be
  rejected from refinement.


  
Default: 0.5
   





GRADIENT



usage:   GRADIENT <GRADMAXR >


 

  Spots with a ratio of either background plane gradient (a or b) to
  the average background (ie a/c or b/c) greater than GRADMAXR wil be
  rejected from the refinement.


  
Default: 0.03







NOUSEBOX



usage:    In the initial stages of refinement in the central region of the


   image, the mask defining the peak and background regions of a spot
  will not be used, but the centroid of the whole measurement box is
  found. This improves the convergence of the refinement, but will not
  work if spots are close together.


  
Default: DO use the peak/background mask even in the first stages of
  refinement in the central region of the detector.