detwin is a third-party patch for CrystFEL software, which helps solve twinning problems in SFX crystal indexing.
Method paper ( Liu, H., & Spence, J. C. (2014). The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm. IUCrJ, 1(6), 393-401. )
Software paper(Shi, Y. , & Liu, H. . (2020). Em-detwin: a program for resolving indexing ambiguity in serial crystallography using the expectation-maximization algorithm. Crystals, 10(7), 588.)
First, download CrystFEL package here. Unzip it.
Then, download detwin package from this github repo, unzip it, and go into the folder.
Next, use command ./replaceFile.sh <crystfel-folder-path> to merge detwin source files into CrystFEL package. For example:
Macintosh:~ detwin$ ./replaceFile.sh ../crystfel-0.9.0
Finally, install CrystFEL !
I . Use unix man command for help information.
II. Refer to command line help information : detwin -h.
Syntax: detwin [options]
read from stream file and convert the data to miller indexed FEL Bragg intensities.
output all crystals HKL, even numbered crystals HKL, odd numbered crystals HKL
-h, --help Display this help message.
--version Print CrystFEL version number and exit.
-i, --input=<filename> Specify input filename ("-" for stdin).
-o, --output=<filename> Specify output filename for merged intensities
Default: processed.hkl).
--stat=<filename> Specify output filename for merging statistics.
-y, --symmetry=<sym> Merge according to point group <sym>.
-k, --spacegroupNum=<k> Specify space group number (143~199).
-m, --max-niter=<t> Number of iterations for de-twinning, default is 30
-s --start-after=<n> Skip <n> crystals at the start of the stream.
-f --stop-after=<n> Stop after merging <n> crystals.
-g, --histogram=<h,k,l> Calculate the histogram of measurements for this
reflection.
-z, --hist-parameters Set the range for the histogram and the number of
=<min,max,nbins> bins.
--scale Scale each pattern for best fit with the current
model. Operated before detwining.
--winner-takes-all If set, among all possible twinning modes, only the one
with higest cc to reference model will merge.
Default: all twinning modes merge in a weighted way
--highres=<n> Reject reflections with resolution (A) higher than n
while calculating CC in detwinning, default is Inf.
--lowres=<n> Reject reflections with resolution (A) lower than n
while calculating CC in detwinning, default is 0.
--no-polarisation Disable polarisation correction.
--cc-only Only calculate and display CC between -i and -o hkl file
--min-measurements=<n> Require at least <n> measurements before a
reflection appears in the output. Default: 2
--min-snr=<n> Require individual intensity measurements to
have I > n * sigma(I). Default: -infinity.
--min-cc=<n> Reject frames with CC less than n. Default: infinity.
--max-adu=<n> Maximum peak value. Default: infinity.
--min-res=<n> Merge only crystals which diffract above <n> A.
--push-res=<n> Integrate higher than apparent resolution cutoff.
--write-assignments Write reindexed results of the crystals in original
=<filename> file to filename.
(only packages with version >= 0.8.0 have the following options)
--add-operators=<op> Add twinning operators manually, such as '--add-operators=
-h,-k,-l/k,h,l'. DO NOT add space between characters !
--write-stream=<fn> Write reindexed stream file to fn.
