Start dtprocess by selecting Utils / dtprocess in the
dtdisplay menu bar. If desired, select File / Open ... in the dtprocess menu bar to load different default input values that were saved in a previous session.
Select the dtprocess window, set Flow chart mode to
Auto strategy if it is not already set.
Select Write dtprocess.head. This automatically finds spots,
indexes, refines and determines a strategy from the current menu settings.
You can save current dtprocess menu settings with
File / Save as... for later use.
Perform steps 1-3 above or type dtprocess your_image_file &.
Set Flow chart mode to Manual.
In the Setup menu, check that the detector position is correct
(Det dist, Det swing, Direct beam). Use
dtdisplay (Edit / Edit (erase...) mode) to mask the pixels in
the beam stop shadow, then File / Save as.... Change Non-uniformity
type to Simple mask and enter the saved mask file. Select Write
dtprocess.head.
Select Find in the flowchart. Select the image or images to search
for spots from the Images list. Set Sigma, Minimum, and
possibly other spot finding criteria, then select Run find. Review the
found spots in dtdisplay.
Select Index in the flowchart. Select User chooses solution.
If you know your spacegroup, set it in Spacegroup num. Select Run
index. Enter desired solution number in the Input: field. If the
desired lattice is not listed, select Abort, increase Max residual
and re-run (or see manual). Since dtindex picks the lowest spacegroup
number consistent with the Bravais lattice, you may wish to change the
spacegroup number. Select Edit / Edit header items ... / Crystal
properties to change the spacegroup. Often it is advantageous to index with spots from a single image.
Select Refine in the flowchart. Select one of the desired
Macros, such as Fit All or select
Interactive dialog to manually select items to refine. Select
Run refine. It is advantageous to refine with reflections from 2 images that are 90 degrees apart in rotation. Repeat until satisfied.
Select Predict in the flowchart. Select the image to predict
spots in. Set the Crystal mosaicity if desired. Select Run
predict. Examine the predictions in dtdisplay. Adjust mosaicity or repeat refine until a good match is obtained.
Select Strategy in the flowchart. For very fast, but approximate
results, set Cell length scale factor to 0.3. Set the desired
Resolution range (default of 0,0 means go to edge of detector).
Select Run strategy.
dtprocess: Integration and Scaling for first-timers
Start dtprocess as above. Set Flow chart mode to
Auto run next. Select Write dtprocess.head.
OR
If the first image to integrate is not the same one used above, then it is
safest to repeat the find, index, and refine steps. Select Predict in
the flowchart. Set Crystal mosaicity, then Run predict. Repeat
with different values of mosaicity until mosaicity is correct. Select
dtpredict.head in the header list. Select Integrate in the flow
chart.
Select the images to integrate in the Images list (i.e. select
Select all).
Set the Resolution range to integrate. If 0,0 is used then the
entire area of the detector will be integrated.
Set the Box size, use 4-6 times the spot size as listed in the
dtfind.log output (View / Log file ...) for starters or choose
a box size by examining the spots with dtdisplay. Boxes should not extend further than to the center of neighboring spots.
Set Padding to 1 for wide-sliced images and to 2 or 3 for fine-sliced
images.
Set Profile size to 0,0 to let dtprocess pick a profile size
for you.
Set Images per batch to 2 for viruses, 2-3 for most proteins, and
10-20 for small molecules.
If you want to automatically scale the reflections after integration, set
the Flow chart mode to Auto run next.
Select Run integrate. After integration is done, if you did not
scale the reflections, select Scale/Average in the flowchart, then
select Run scale. To get Chi**2 to 1, adjust Weight multiplier and Weight addend and re-run. If available, use dtreqab.ref with Cycles 1, and Absorption correction None to save time when adjusting sigmas this way.