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Re: Base coordinate set for CBF, and Minimal headers.

Paul Ellis and I are close to the end of our cycles on the API, so I'll
include as much of this material as I have in the documentation of CBFlib
0.6, and that will include a try at a proper DDL2 dictionary.  People
should be aware that Paul and I intend to propose a signigicant change in
the binary header, deleting some fields which are taken care of by the new
MIME headers.
  -- Herbert 

=====================================================
****                BERNSTEIN + SONS
*   *       INFORMATION SYSTEMS CONSULTANTS
****     P.O. BOX 177, BELLPORT, NY 11713-0177
*   * ***
**** *            Herbert J. Bernstein
  *   ***     yaya@bernstein-plus-sons.com
 ***     *
  *   *** 1-516-286-1339    FAX: 1-516-286-1999
=====================================================

On Mon, 28 Dec 1998, Robert Sweet wrote:

> I'm attaching material I've composed over the last few weeks for the CBF
> effort.  I've tried to be concise, and as a consequence may have made
> things too brief to be understood.  I need esp. for Jim Pflugrath and
> Zbyszek Otwinowski to examine all of this to see if it makes sense and is
> usable.  I'd hoped to find time to write more complete definitions to help
> John Westbrook in the writing of dictionary entries, but don't have the
> leisure for that right now. 
> 
> I'll look forward to hearing comments soon.
> 
> Regards,
> Bob Sweet
> ------------------------------------------ 
> 
> 
> Proposal for Details of the contents of headers for imgCIF/CBF files
> --------------------------------------------------------------------
> 
> R.M. Sweet
> 24 Dec 1998
> 
> Contents (look for * to find sections):
>      1. Base coordinate set to describe the experiment
>      2. Minimum optimal parameter set for data reduction
> 
> * Discussion of base coordinate set for crystallographic
> goniometers.  
> 
> The Base Coordinate system should be based on the principal axes of the
> goniometer, not on the orientation of detector, gravity, etc.  The actual
> orientation of goniometer axes will be defined by refinable vectors,
> defined by this basis set. 
> 
> Descriptions of the axes follow.  Each axis is right handed -- that is, as
> one views the object to be rotated from the tail of the vector being
> defined, the rotation is clockwise. 
> 
> Axis 1 (X): The mechanical axis, pointing from the crystal to the
> principal axis of the goniometer.  This is the only axis, the direction of
> which is strictly connected to hardware.  The zero point of axes that
> rotate about this axis (crystal, detector) is referred to axis 3 (Z). 
> This rotation direction matches the sense of most commercial goniometers. 
> 
> Axis 3 (Z): The source axis, pointing from the crystal towards the source. 
> It lies in the plane of Axis 1 (X) and the source, and is perpendicular to
> X. 
> 
> Axis 2 (Y): Completes the right-handed system. 
> 
> Other axes must be defined to describe the experimental setup.  I'll try
> to define something that is more-or-less consistent with CIF.  I believe
> that we may have only single values with each tag. 
> 
> Crystal Goniometer -- We can define the goniometer with optional
> parameters (description, axis names) and obligatory ones.  The supposition
> is that the axes are nested, and rotations are right- handed, as above. 
> That is, rotation matrices for the three axes (1,2,3) should be applied in
> the order 1.2.3.x = x'. 
> 
> Here are some rough names for specifications and descriptions of the
> entries. 
> 
> xtal_gon_description eulerian; Or kappa, unknown
> 
> I suppose there should be:
> xtal_gon_num_axes: 3
> 
> Then: 
> 
> xtal_gon_axis1 omega;
> xtal-gon_axis2 kappa;
> xtal_gon_axis3 phi;
> 
> xtal_gon_unit1 deg;
> xtal_gon_unit2 deg;
> xtal_gon_unit3 deg;
> 
> This is awkward, but we need nine entries to define the directions of the
> goniometer vectors.  Can one use loops? 
> 
> xtal_gon_vector11 1
> xtal_gon_vector12 0
> xtal_gon_vector13 0
> xtal_gon_vector21 -.643
> xtal_gon_vector22 0
> xtal_gon_vector23 -.766
> xtal_gon_vector31 1
> xtal_gon_vector32 0
> xtal_gon_vector33 0
> 
> These represent (I believe) the directions of rotation vectors for a kappa
> goniometer with the kappa axis inclined by 50 deg from the omega axis. 
> 
> Finally, how about 
> 
> xtal_gon_gravity  0 -1 0
> 
> Detector Goniometer -- Should be similar to the x-tal goniometer, except
> that there may be rotations and translations.  Do we need to say which of
> these the vectors represent?  For generality, prob. we do.  I give up,
> somebody else figure out how to get the values into a CIF and how best to
> name them.  Note that there should be either X and Y translations or a
> beam center.  The catch with the former is that one must define what is
> the default center with translations eq. 0.  We'll use the latter.  That
> is, the beam is allowed to go off the edge of the detector.  Also since we
> want to treat detector images as either distortion corrected or not, we'll
> define the beam center as being in distortion-corrected mm from the (0,0)
> corner of the detector (axis directions are lab X,Y). 
> 
> det_gon_num_axes: 4
> 
> det_gon_axes: twotheta, roty, rotz, tranz; The last is negative of
> distance.
> 
> det_gon_axis_type: R, R, R, T
> 
> det_gon_units: deg deg deg mm 
> 
> det_gon_vectors: 1 0 0   0 1 0   0 0 1    0 0 1 
> 
> Source Geometry -- The x-ray beam must travel through the crystal, and the
> source/omega plane defines the origin of rotation for the X axis, but the
> source need not be perpendicular to the X axis.  Therefore, there should
> be refinable parameters where the Y component is fixed at zero: 
> 
> source_vector 0 0 1
> 
> where the X and Z components can be sin and cos, resp. of the angle the
> source actually makes with the X perpendicular, and the second variable is
> always 0.
> 
> 
> * Discussion of Minimum optimal parameter set for data reduction
>  
> Certain parameters are defined by the experiment and will be "known" by
> the data-collection software, certain will be "site specific" and could be
> inserted into a file header while the data are being written, or perhaps
> they should be read in before data reduction as a "site" file.  Others
> should be represented by suitable defaults within the program but in some
> cases could be written into a header.  Finally, some will be known only to
> the user -- things like the space group. 
> 
> We presume that correct values for all the experimental geometric
> parameters described above will be in the header.  Here are additional
> parameters that should be known to the data-collection software, and
> therefore should be written into every header.  These should be sufficient
> for data reduction with suitable defaults or a few site-specific
> parameters, with definitions:
> 
> source_wavelength  1.07; In Angstroems
> 
> source_polarization_vector 0 1 0; This is perpendicular to both the source
> vector and the polarization vector of the x-ray beam.
> 
> source_polarization_value 0.95; Conventional definition -- 0.5 for
> unpolarized, 1.0 for perfectly polarized.
> 
> detector_beam_center 105.1 98.7; in distortion-corrected mm relative to
> (0,0) corner of detector. 
> 
> detector_readout -Y +X; define directions of fast then slow readout axes,
> relative to the lab XY system.  This does not define the (0,0) corner of
> the detector, which is defined by the lab XY system. 
> 
> detector_gain 2.3;  The (x-ray photons)/ADU conversion factor -- should be
> wavelength dependent. 
> 
> detector_resolution_dmin 1.8; Calculated from detector geometry and
> wavelength. 
> 
> scan_rotation_axis_name omega
> 
> (How cute do we want to be here?  Do we want, say, to allow
> rotation about phi when omega and kappa are not at zero?  Should
> we say that either this below or the one above should be given
> since one implies the other?)
> 
> scan_rotation_axis_vector 1 0 0;
> 
> scan_xtal_gon_sweep_start 200.0 -40.0 127.5; start position for
> the sweep of images of which this is one.
> 
> scan_sweep_range 0.0 20.0; Relative to the start position above. 
> scan_sweep_increment 0.10;
> 
> scan_sweep_integration_time  3.0; In seconds.
> 
> scan_sweep_template '/data1/bnl/xtal1/mad_L2_###.img';
> 
> scan_sweep_filnum 0; Beginning filenumber for the range defined
> above; ending number can be calculated.  
> 
> scan_filenum 18; The file number for this file
> 
> These below are actually redundant.  Should we leave them out? 
> scan_filename ''/data1/bnl/xtal1/mad_L2_018.img';
> 
> scan_xtal_gon_start 201.8 -40.0 127.5;
> 
> scan_start_angle 1.80; Starting point relative to the range and
> increment above.
> 
> 
> Defaults to go into "site" file:
> 
> Integration box sizes, for peak, buffer area, background-
> integration box, etc.
> 
> Beam crossfire.
> 
> Parameters input by user:
> 
> Space Group or Bravais Lattice
> 
> 
> 
> 
> 
> =========================================================================
> 	Robert M. Sweet			E-Dress: SWEET@BNL.GOV 
> 	Biology Dept.			Phones:
> 	Brookhaven Nat'l Lab.		516 344 3401  (Office)
> 	Upton, NY  11973		516 344 5642  (Beamline at NSLS)
> 	U.S.A.				516 344 3407  (Facsimile)
> =========================================================================
> 
> 
>

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