Tips and Tricks in Crystallography - Diffraction

Recommended Readings on Data Collection:
http://www.px.nsls.bnl.gov/courses/papers/ZD_EG_papers.html

David Garboczi (NIAID): Our Experiences with the Data Reduction Program XDS
        Let me tell you about our experiences with the data reduction program XDS as an alternative to the more widely used software packages. It is run by a script that is detector-specific and there are examples on Wolfgang Kabsch's web site. We find it to be flexible and easy to use, which allows more experimenting with the raw X-ray data to achieve the best datasets. (Full Article)

Need an image processing software that builds three-dimensional profiles? Try XDS. For an easy start, see INTEGRATE by Kay Diederichs.

Recommended viewing: How long will my crystal last?

Mr. Jerry Alexandratos (NCI): Post-crystallization soaking. Do you have poorly diffracting crystals?  Don't throw them out. Try post-crystallization soaking by adding 1.5-2 M (NH₄)₂SO₄ with or without several percent of PEGs such as 3350. You can also try slightly dessicating drops with crystals.  (I did not note down who mentioned these procedures. My apologies, as well as my thanks for the tips.) 

Dr. Lothar Esser (NCI): Denzo, XDisplayF, Scalepack. In case you are not yet using HKL2000 which is a GUI (graphical user interface) that controls denzo, xdisp and scalepack you should consider getting a copy of it. Officially it is not in general distribution (current version 0.97.638) but since the development of this program is funded by NIH, there is no problem for NIH crystallographers to get a pre-release free of charge. Routine and non-routine data reduction can be done very efficiently if you (or your student) are new to data processing but even more so if you have worked your way through the input files for denzo and scalepack before. Indexing and integrating of data is effortless and so is data reduction.

Is everything done by a push on a button? Well, you still have to manually adjust the error-of-scale factor until the overall χ² is about 1.0. So for straightforward data sets, i.e. data sets that do not require much adjusting of the error bins, I have been using a utility program that does nothing more than running scalepack until the χ² is 1 within a user-defined limit. To get the final graphical analyses you may run scalepack from within HKL2000 one more time with the updated reject file and the refined error-of-scale factor. In many cases this saved me a lot of time. (Let me know if you want to have a copy of this program)

Have you ever run xdisp on a remote computer and redirected it to an X display on a SGI? In that case you might have noticed that the fonts of xdisp are too large. In fact some buttons on the zoom window are missing. This problem can be solved by giving the x font server a different path to font files. Try this before you open xdisp on the SGI (the local machine):

set FONT_P=”/usr/lib/X11/fonts/misc/,/usr/lib/X11/fonts/75dpi/”

set FONT_P=”${FONT_P},/usr/lib/X11/fonts/100dpi/,/usr/lib/X11/fonts/Type1/”

set FONT_P=”${FONT_P},/usr/lib/X11/fonts/Speedo/,/usr/lib/X11/fonts/CID”

xset fp $FONT_P