dtprocess on-line help

Copyright (c) 1997 Molecular Structure Corporation

Setup calibration and scan info

The Setup menu is used to modify the calibration information and scan template stored in the selected image or header file and to write an initial header dtprocess.head for subsequent dtprocess steps. Controls are available to change:

Use the Edit header items... command from the menubar for more complex header edits.

Select a header file from the top list or an image file from the bottom list.

Select the Non-uniformity type from the option menu.

Select the Spatial distortion type from the option menu.

Set the Direct beam position in pixels when the detector is perpendicular to the source and its swing and translation values are all 0. You may use dtdisplay to view images and determine the direct beam position.

Set the Scan template.

Setup menu options

Non-uniformity type
Select the method of non-uniformity of response correction that you wish to apply to images.
None
No correction will be applied.
Simple mask
No correction will be applied, but a separate image file will be used to flag bad pixels, such as those in the shadow of the beam stop. Any pixels with a value of 0 in this separate file will be flagged as bad to d*TREK. Use dtdisplay with the Edit / Erase (edit nonunf) mode to create the mask file and save it with File / Save as.... Then specify the mask file in the Non-uniformity file field.
Dark & Nonunf
Each pixel will be corrected by subtracting a dark current value and multiplying by a non-uniformity scale factor. The dark current value comes from an image specified in the Dark file field. The non-uniformity scale factor comes from an image specified in the Non-uniformity file field. Bad pixels are flagged in the non-uniformity file.
Spatial distortion type
Select the method to convert from detector pixels to millimeters and vice versa.
Simple
Pixel positions are simply multiplied by a scale factor to get millimeters. Specify the pixel size in millimeters in each direction in the Pixel size (mm) fields.
Interp. tables
Pixel positions are converted to millimeters by lookup and interpolation tables created by the calibrate program. Specify the interpolation tables basename in the Interp table basename field.
Direct beam (px)
Specify the pixel position that the direct beam would impinge on the detector when the detector has no rotations and no translations applied. This is, the swing angle of the detector is 0 and the translations of the detector (X/Trans1 and Y/Trans2) are 0. If these values are incorrect or not compensated by the detector X and Y translations, then indexing, refinement, and prediction will be virtually impossible. The single most frequent reason for failure to index and refine crystal properties is incorrect values specified here.
Master resolution
Specify the resolution limits in Angstroms for other menus (except Strategy). The resolution limits in the Find, Index, Refine, Predict, Integrate, and Scale menus are set to these values if BOTH are non-zero AND you select 'Write dtprocess.head'. The default of values of 0.0, 0.0 usually will mean the entire resolution range on the image will be used.
Spacegroup (maybe)
Specify a 'suggested' spacegroup number to use in the Index menu. When 'Write dtprocess.head' is selected this number is copied to the Index menu. It is not copied to the crystal properties in the header. The default is normally 0 which lets the program select the spacegroup.
Scan template
Specify the scan template which is an image filename with question marks (?). The ?s will be filled in by the sequence numbers of images contained in the scan to generate the image filenames. Images that match the scan template will appear in the Images list.