"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.

Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data
3D ED data sets of 5 compounds and JANA refinement files of 12 compounds

Relevant tools:

PETS2: data reduction and analysis of electron diffraction patterns

Download program and access step-by-step tutorials at http://pets.fzu.cz/

Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst. B75, 512–522 (2019). DOI: 10.1107/S2052520619007534

JANA2006: crystal structure model refinement program

Download program from http://jana.fzu.cz/ and access step-by-step tutorials at http://pets.fzu.cz/

Results here were obtained with JANA2006. We recommend using JANA2020.

Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. Z. Kristallogr. 229, 345–352 (2014). DOI: 10.1515/zkri-2014-1737

DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives

Program automatically included in JANA2006/JANA2020

Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Cryst. A71, 235–244 (2015). DOI: 10.1107/S2053273315001266

3D ED data sets:

STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at http://pets.fzu.cz/.

α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)

natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)

cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)

abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)

STW_HPM-1, continuous-rotation (1 data set, room temperature)

STW_HPM-1, continuous-rotation (1 data set, T = 100 K, cryotransfer)

JANA refinement and CIF files:

CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details.

JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included.

α-quartz

albite

mordenite

natrolite

STW_HPM-1

cobalt aluminophosphate (CAP)

CAU-36

α-glycine

carbamazepine

(+)-limaspermidine

abiraterone acetate

MBBF4

For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files.

Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.