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Base coordinate set for CBF, and Minimal headers.

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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