Software fayre: raw data hkl file
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1 Software fayre: raw data hkl file Matteo Alvaro This work was supported by: NSF grant - Earth Sciences Division EAR Department of Geosciences, Virginia Tech. College of Science, Virginia Tech. Topics Software fayre: going from raw data to hkl file Experimental and data processing challenges PD Vs. CCD Choice of the right software Quick overview of the software available Practical session Area detectors (CCD) Point detectors (PD) Oxford diffraction (Diego Gatta) Bruker (Tonci Balic-Zunic ) STOE (Andrzej Grzechnik, Karen Friese) XDS (Andrzej Grzechnik, Karen Friese) WinIntegrstp (Ross Angel)
2 Practical sessions SOFTWARE FOR AREA DETECTOR Oxford diffraction (Diego & Fabrizio) Bruker (Tonci) STOE (Karen & Andrzej) XDS (Karen & Andrzej) SOFTWARE FOR POINT DETECTOR WinIntegrstp (Ross) Intensity data collection Crystallographic basis Data Collection Data Collection Data integration Crystallographic basis Data integration CCD is shoot first and ask questions later R.J. Angel
3 Intensities at high pressure: Challenges Very precise data to measure very small changes in structures at high pressures. Absorption by DAC s components Conventional DAC with Beryllium seats, Rings steel gasket Diffracted intensities reduced Scattering by DAC s components Highly structured background Double diffraction Limited access 1/3 or less than the entire dataset Limited equivalent reflections Rejection of aberrant intensities Low signal Marburg-type DAC with Highly rhenium structure gasketbackground 350um Intensities at high pressure: Solutions Point detector Experimental Accurate peak positions (offset) Multiple scans Higher collimation Slits settings Detector distance Data processing Optimized scan speed Optimized integration algorithms (Step scans) Profile fitting Recovery of weak data Area detector Experimental Poor peak positions (no offset) Beryllium cone (post integr. corr) Exposure time/generator power Detector distance Data processing Masking solutions (global, local) Multiple indexing (diamonds, Qz) Overlap checking Every reflection profile in a data set must be visually examined by the 350um experimentalist (open to human misjudgement and errors!!)
4 Integration: Area detectors Area detector Data processing Masking solutions Global, local Static, dynamic Multiple indexing Diamonds, Qz Overlap checking 3D indexing algorithm 350um Integration: Point detector Diamond Reflection overlap Double-diffraction Weak data M=measured at the minimum speed R=Rejected R= Fails at the test of the intensity ratio 1=first attempt Point detector Data processing Diamond reflections Double-diffraction Optimized scan speed Optimized integration algorithms (Step scans) Profile fitting Recovery of weak data 2D indexing algorithm 350um
5 What to know: CCD and point detectors Point detector Pros Better/lower background Better handling of the refls Recovery weak data Avoid bad reflections Reflections Offsets Optimised scan speed Optimized integration algorithms (Step scans Higher collimation (small cells) Cons Long data collections UB matrix determination Long Not allowed by all the software Possible misindexing Area detector Pros Quick Peak hunting Fast intensity data collection Large number of reflections High Redundancy High background Diffuse scattering Approx equal intensities Equal scan speed Static images No handling of the refls No refls offsets Black box CCD and point detectors: Practical example Structure refinements data Bond distance values Good agreement between DAC- PD and CCD in air Almost in agreement DAC-PD DAC-CCD Bond distance esd s Always higher value on CCD Agreement betweend CCD in air and PD in DAC Data obtained on the same instrument with two different detectors
6 Commercial software available XDS CCD XDS software Exchange capabilities Support many detector format Pilatus, Marr555, Marr345, marccd, R-AXIS II, R-AXIS IV, R- AXIS IV++, RAXIS-V, SATURN 92, CRYSALIS, STOE, SIMENS HKL conversion to different format Indexing optimization Learned reflection profile Spatial correction at each pixel of a detector Centering the diffraction peaks Refine orientation matrix (UB) Defines the obscured regions of the detector Post integration feature Wolfgang Kabsch, author of the th publication on Crystallography Journals Online.
7 CCD XDS software Pro Free of charge High compatible with several instruments (home labs and large scale facilities) High level useful high pressure features No reciprocal space reconstruction No incommensurate phases Not so much interactive (black box) CCD STOE software Exchange capabilities Support many detector format Stoe IPDS II, Stoe IPDS 2T, IPDS 2T dual beam, Pilatus, HKL conversion to different format Indexing optimization Overlap Check Masking (beam stop, Be ring and diamond peaks) Multi orientation matrix feature, up to 6 matrices (twins, diamond overlap etc..) Refine orientation matrix (UB) Defines the obscured regions of the detector (each frames has it own mask) Incommensurate structures Reciprocal space reconstruction Post integration feature
8 CCD STOE software Pro Free of charge High level useful high pressure features Reciprocal space reconstruction Quite much interactive (allowed a lot of user intervention) Not Highly compatible with several instruments Hand made masking of the shadowed areas of the detector Use of the mask to optimize the integration profile CCD Oxford Diffraction software Exchange capabilities Support many detector format Marr555, Marr345, marccd, HKL conversion to different format Indexing optimization Centering the diffraction peaks Refine orientation matrix (UB) Defines the obscured regions of the detector Masking (beam stop and Be ring) Multiple cells handling (twins, diamonds etc ) Post integration feature
9 CCD Oxford Diffraction software Pro Free of charge Compatible with different instruments (home labs and large scale facilities) High level useful high pressure features No feature for the masking of a single reflection (e.g. Diamond peaks) Not extremely interactive CCD Bruker software (SaintPlus) Exchange capabilities Support many detector format Marr555, Marr345, marccd, Pilatus coming soon (other detector formats via conversion software) HKL conversion to different format Indexing optimization Hand picking of the reflections Centering the diffraction peaks Refine orientation matrix (UB) Multiple cells handling Masking areas of the detector Post integration feature
10 CCD Bruker software (SaintPlus) Pro Comes with the instrument ($$$) Compatible with many instrument (Thanks to the conversion software) Hand picking of the reflections Tricky handling of the unit cell parameters and multiple cells Difficult handling of the overlapping (diamond peaks) Not so much interactive (black box) Very recommended OLD versions of the software!!! PD WinIntegrSTP software Exchange capabilities Support many point detector format Xcalibur, Xscans, STOE, Philips Febo, CAD4, old version Single HKL (shelx or Rfine formats) Indexing optimization Step scans integration Visual examination of the refls Centering the diffraction peaks Refine orientation matrix (UB) Different background refinements choice Post integration feature No post integration features Need other softwares Angel R.J. (2003) J. Appl. Cryst. 36,
11 PD WinIntegrSTP software Pro Free of charge High compatible with several instruments (home labs and large scale facilities) Mainly designed for High pressure data integration Continuously developed Flexible!! Please ask to Ross.
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