Data Processing

Processing/indexing first frame:

Denzo must be installed and aliased properly:

Here are some example aliases that I use for different formats:

< 11 otter /buckler/DENZO> which denzo
denzo:   aliased to /keck2/people/kalyan/HKL196/denzo
< 16 otter /buckler/DENZO> which xdisp2
xdisp2:          aliased to /keck2/people/kalyan/HKL196/xdisp raxis
< 17 otter /buckler/DENZO> which xdisp4
xdisp4:          aliased to /keck2/people/kalyan/HKL196/xdisp raxis4 100
<15 otter /buckler/DENZO> which xdispq4
xdispq4:         aliased to /keck2/people/kalyan/HKL196/xdisp ccd adsc unsupported-q4

Edit auto.dat, refineone.dat and refine.dat files with proper parameters and so that they point to the image files properly

In general, a processing session with Denzo/Xdisplayf/Scalepack involves the following steps: i) view an initial image through the Xdisplayf GUI, ii) find strong peaks in the image, iii) use those reference peaks to auto-index the crystal through the Denzo program, iv) refine the cell parameters through a Denzo refinement of a single image (@refineone.dat), and v) extend the Denzo refinement to all images (@refine.dat) which results in output files (*.x) of indexed spot intensities for each image.

Example auto.dat files:

Example Denzo refinement files:

The Denzo/Xdisplayf/Scalepack manuals should be consulted when editing the above command files; but, in general, the following will be edited in auto.dat files for a new run: beam center, wavelength, filename, sector, distance, resolution limits, mosaicity, and space group. For initial autoindexing, indicate space group p1; thereafter, and in preparation for final image processing, the proper spacegroup should be input. Note also that the mosaicity should be slightly higher than the correct value. Usually the whole set of images are processed in Denzo, scaled in Scalepack (see below), and if the refined mosaicity from Scalepack is much different from that used in the Denzo processing, the mosaicity value in the auto.dat file should be changed and new individual, processed image files should be generated by carrying out a new Denzo run. I typically use a mosaicity value 0.05 - 0.10 deg above the value found after refinement in Scalepack (higher to avoid losing some reflections -- they will be thrown out later during scaling -- see Scalepack manual).

The refineone.dat command file specifies a stepwise refinement for a single image, where shells of increasing resolution are selected. The commands in the refine.dat file are identical to those in the refineone.dat file except for the additional statements that extend the refinement for all images (start refinement, calculate go, end of pack; see above files).

To actually start the image processing, open up two windows: one for Xdispf and a second for Denzo. Currently, xdisp and denzo must be run from lion (rlogin or telnet to lion first). In one window, start xdisp with the appropriate alias and a single image file, e.g.:

< 3 lion /buckler/DENZO> xdispq4 ../smdr_1_001.img

where the img files reside one level up in the directory tree.

In a second window, Denzo is started with the appropriate alias (e.g, "denzo"). Then:

The image file should now be visible in the xdisp display gui. Select the Peak Search button which generates a file of best peaks (peaks.file). The number of found peaks can be incresed or decreased (More Peaks/Fewer Peaks).
Run @auto.dat in the Denzo window which uses the peaks file to auto-index the reflections.
If the predicted spots match well, the parameters can be refined with @refineone.dat.
Edit the auto.dat file and expand the range of images (sector).
Run the @auto.dat file again, and then run @refine.dat, which will process all images, generating the *.x output files for scaling in scalepack.

Data scaling with Scalepack:

Here is a typical Scalepack refinement file:

scale.sh

The "fit crystal" parameters should match the number of free parameters for a particular spacegroup (e.g., for P21, alpha=gama=90 deg; therefore, only beta is fit, whereas a*,b*,and c* are all fit since each are unique).