[ccp4bb]: Re: MOSFLM and CCD images

[Marian Szebenyi <dms35@cornell.edu>]

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Leslie A. wrote:

> 
> Using MOSFLM to process data from ADSC Quantum4 and Mar CCD detectors
> =====================================================================
> 
>    I believe that there may be "example scripts" for processing data
> from CCD detectors that use the generic form for the DETECTOR or
> SCANNER keyword, and which therefore are not optimal for processing
> these type of images. For example, data from the Mar CCD detectors may
> be processed with the keywords:
> 
> SIZE            2048 2048   HEADER 1
> SCANNER         ROTATION HORIZ ANTI FAST HORIZ ORIGIN UR CIRCULAR
> PIXEL           0.079182
> LIMITS          XMAX 82.5 YMAX 82.5 RMAX 82.5 RSCAN 82.5
> 
> All of these keywords can be replace with the single keyword:
> 
> DETECTOR MARCCD
> 
> The problem with using the generic form of the DETECTOR keyword is
> that the information in the file header (wavelength, crystal to
> detector distance, two-theta value and oscillation angles) is ignored
> by the program, so all of these parameters have to be input
> explicitly by the user.
> 
> In addition, when using DETECTOR MARCCD keywords the program will
> determine from the image if this is a small or large MarCCD detector,
> and automatically assign the correct pixel size (which can vary
> slightly from detector to detector) and the value assigned to pixels
> outside the active area of the detector.
> 
> The same comments apply to images from the ADSC quantum 4 detector,
> which should be processed using the keywords:
> 
> DETECTOR ADSC

This is true, PROVIDED that your detector is in the standard orientation
and your spindle is rotating in the expected direction. You should at
least be aware that you may need the REVERSEPHI argument. Moreover, you
can get MOSFLM to read the file headers by specifying 'TYPE MARCCD' or
'TYPE ADSC' on a generic SCANNER line. If input lines are being
generated from a graphical interface, the fact that there are 4 instead
of 1 of them is not important. Hence, the DPS/MOSFLM package chooses to
produce lines such as:

SCANNER ROTATION HORIZ CLOCK FAST horizontal ORIGIN UR RECT TYPE ADSC
SIZE 2304 2304
PIXEL 0.0816 0.0816
LIMITS RMIN 5 RMAX 134.1 XMAX 94.9 YMAX 94.7 XSCAN 94.0 YSCAN 94.0

This form is more general (for instance, it can deal with a detector on
its side), without losing the capability to read the file headers.

> 
> The BIAS keyword
> ================
> 
> It should not be necessary to use the BIAS keyword.

Quite true. Anyone using DPS/MOSFLM might want to modify the
MosflmIntegrate.com script accordingly. Will be fixed in the next
version.

> 
> Autoindexing using the ADSC interface
> =====================================
> 
>    Autoindexing using the ADSC GUI uses the DPS autoindexing algorithm
> from Michael Rossmann's laboratory. The same algorithm (and code) is
> used in MOSFLM, but there is an important additional step in the
> MOSFLM implementation that refines the cell parameters that come from
> the DPS indexing. The refinement step makes the autoindexing
> significantly more robust. If the autoindexing using the ADSC GUI
> fails, it is worth trying to autoindex using MOSFLM.

Also true, at least until the next version of DPS comes out - a new
refinement program is in the works which may (we hope) do even better
than MOSFLM.
  

Marian Szebenyi

DPS support, Cornell U.