advanced crystal structure analysis using xds with small...

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Advanced Crystal Structure Analysis

Using XDS with Small Molecule Data

Tim Grüne

Georg-August-Universität

Institut für Strukturchemie

❤tt♣✿✴✴s❤❡❧①✳✉♥✐✲❛❝✳❣✇❞❣✳❞❡✴⑦t❣

[email protected]

November 13, 2013

Tim Grüne XDS: small molecule data 1/39

http://shelx.uni-ac.gwdg.de/~tg

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Overview

• XDS Availability and Documentation

• XDS Basics: ❳❉❙✳■◆P and the ❏❖❇-card

• Parameter Refinement

• Indexing: Difficult cases like multiple lattices, poor diffraction

• 2 Small Molecule Examples: Synchrotron / ❙▼❆❘❚ data (s❢r♠t♦♦❧s)


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The XDS Resources

Author W. Kabsch

Now distributed by K. Diederichs

availability:

XDS ❤tt♣✿✴✴①❞s✳♠♣✐♠❢✲❤❡✐❞❡❧❜❡r❣✳♠♣❣✳❞❡✴ main program suite

Wiki and auxiliary programs ❤tt♣✿✴✴str✉❝❜✐♦✳❜✐♦❧♦❣✐❡✳✉♥✐✲❦♦♥st❛♥③✳❞❡✴①❞s✇✐❦✐✴

GUIs

• xdsGUI ❤tt♣✿✴✴str✉❝❜✐♦✳❜✐♦❧♦❣✐❡✳✉♥✐✲❦♦♥st❛♥③✳❞❡✴①❞s✇✐❦✐✴✐♥❞❡①✳♣❤♣✴❳❉❙❣✉✐ very good graph-

ical display of statistics

• Xdsapp ❤tt♣✿✴✴✇✇✇✳❤❡❧♠❤♦❧t③✲❜❡r❧✐♥✳❞❡✴❢♦rs❝❤✉♥❣✴❢✉♥❦♠❛✴s♦❢t✲♠❛tt❡r✴❢♦rs❝❤✉♥❣✴❜❡ss②✲♠①✴

①❞s❛♣♣ optimised for data collection at BESSY - fast for standard cases.


http://xds.mpimf-heidelberg.mpg.de/

http://strucbio.biologie.uni-konstanz.de/xdswiki/

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/xdsapp

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/xdsapp

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Documentation

• Very well organised html-documentation

• Every STEP documented

• Every keyword documented

• Coordinate systems are explained


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XDS Programs

xds par Main program for data integration

xscale par scaling program for multiple datasets

cellparam Weighted average unit cell parameters from several runs


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Templates

• Templates of input scripts for all supported detector formats

• Only very few adjustments necessary to get started

• Beamlines often generate appropriate input scripts

• ❣❡♥❡r❛t❡ ❳❉❙✳■◆P from XDSwiki for MARCCD, ADSC,

and the Pilatus 6M

• It is worth learning how to set it up from scratch!

❤tt♣✿✴✴str✉❝❜✐♦✳❜✐♦❧♦❣✐❡✳✉♥✐✲❦♦♥st❛♥③✳❞❡✴①❞s✇✐❦✐✴✐♥❞❡①✳♣❤♣✴●❡♥❡r❛t❡❴❳❉❙✳■◆P


http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP

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Benefits and Malefits

Benefits Malefits

• robust indexing and robust integration

• integrate synchrotron data

• fast! (parallelised)

• optimised for Dectris’ Pilatus Detectors

• easy to fine-tune parameters

• not dedicated to twinned data or multiple lat-

tices (treatment of overlaps)

• manual setup

• little graphical output

• no global parameter refinement for multiple

runs


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Program Control: ❳❉❙✳■◆P

XDS is controlled by one single input file: ❳❉❙✳■◆P.

• Contains about 100 Keywords of the form

❑❊❨❲❖❘❉❂❱❆▲❯❊

• Only about 10 Keywords must be modified for most data sets

• Most important one:

❏❖❇❂ ❳❨❈❖❘❘ ■◆■❚ ❈❖▲❙P❖❚ ■❉❳❘❊❋ ❉❊❋P■❳ ❳P▲❆◆ ■◆❚❊●❘❆❚❊ ❈❖❘❘❊❈❚

Each name stands for one of the steps XDS carries out during data integration. (❳P▲❆◆ is optional

and corresponds to the BEST [2] or STRATEGY [1] output to report optimal data collection

range(s))

• Name cannot be changed

• Each data set must be run in separate directory to avoid overwriting of files.


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Setting up ❳❉❙✳■◆P (starting from template)

• ❉❊❚❊❈❚❖❘ ❉■❙❚❆◆❈❊❂ ✸✵✵✳✵ ✦✭♠♠✮

• ❖❙❈■▲▲❆❚■❖◆ ❘❆◆●❊❂✵✳✶ ✦❞❡❣r❡❡s ✭❃✵✮

• ❳✲❘❆❨ ❲❆❱❊▲❊◆●❚❍❂✶✳✼✼✶✷✵ ✦❆♥❣str♦❡♠

• ◆❆▼❊ ❚❊▼P▲❆❚❊ ❖❋ ❉❆❚❆ ❋❘❆▼❊❙❂✳✳✴s❤❡❧①✶✹✴❙ ✶ ❄❄❄❄✳❝❜❢

• ❉❆❚❆ ❘❆◆●❊❂✶ ✹✾✵✵

• ❖❘●❳❂✶✶✽✵✳✵ ❖❘●❨❂✶✷✾✾✳✵ ✦❉❡t❡❝t♦r ♦r✐❣✐♥ ✭♣✐①❡❧s✮

Direct beam position at 2θ = 0◦


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Steps of Data Processing

IDXREF

COLSPOT

INIT

XYCORR

CORRECT

INTEGRATE

DEFPIX

Step

SPOT.XDS

XPARM.XDS

INTEGRATE.HKL

input files

SPOT.XDS

XPARM.XDS

FRAME.cbf

SPOT.XDS

ABS.cbf

BKGPIX.cbf

FRAME.cbf

INTEGRATE.HKL

XDS_ASCII.HKL

GXPARM.XDS

output files

(Important)

red: Text files with parameters or data

cyan: control images (use ①❞s✲✈✐❡✇❡r)

black: data files for further processing


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The Steps

❳❨■◆■❚ writes files for positional corrections of the detector plane. Most modern detectors provide

already corrected images so that these to files are normally flat (0).

■◆■❚ determines initial detector background

❈❖▲❙P❖❚ collect strong spots for indexing (❙P❖❚ ❘❆◆●❊)

■❉❳❘❊❋ indexing: unit cell dimensions and crystal orientation

❉❊❋P■❳ set active dectector area (exclude resolution cut-off, beam stop shadow, ice rings. . . )

❳P▲❆◆ (optional) generate “strategy” tables with data completeness

■◆❚❊●❘❆❚❊ extract reflection intensities from frames

❈❖❘❘❊❈❚ applies corrections (polarisation, Lorentz-correction, . . . ), scales reflections, reports data

statistics

The ❈❖❘❘❊❈❚’ed ❳❉❙ ❆❙❈■■✳❍❑▲ is already scaled. Scaling of multiple data sets best done with ❳❙❈❆▲❊.


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Program Flow

• Each step must be passed at least once - the subsequent steps depend on files produced by

the previous steps.

• Each step creates a log-file (❳❨■◆■❚✳▲P✱ ■◆■❚✳▲P✱✳✳✳).

• ■❉❳❘❊❋ is the main hurdle - once unit cell and crystal orientation are determined, integration

usually runs smoothly.

• ❈❖❘❘❊❈❚ summarises the quality of the data.

• Mostly ■❉❳❘❊❋✳▲P and ❈❖❘❘❊❈❚✳▲P should be inspected.

①♣r❡♣ reads both the output after ❈❖❘❘❊❈❚ (❳❉❙ ❆❙❈■■✳❍❑▲) and the output from ①s❝❛❧❡ ♣❛r


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❳❙❈❆▲❊: Multiple Runs

• Simple input script ❳❙❈❆▲❊✳■◆P:

❖❯❚P❯❚❴❋■▲❊❂❇✽❴❑✸✵✳❍❑▲

■◆P❯❚❴❋■▲❊❂✳✳✴❧✶✴❳❉❙❴❆❙❈■■✳❍❑▲

■◆P❯❚❴❋■▲❊❂✳✳✴❧✷✴❳❉❙❴❆❙❈■■✳❍❑▲

• First INPUT FILE: Reference and source for cell and spacegroup

• Usually no further options required


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❳❙❈❆▲❊✳▲P

• Logfile ❳❙❈❆▲❊✳▲P: statistcs table similar to ①♣r❡♣

❉❆❚❆ ▼❊❆◆ ❘❊❋▲❊❈❚■❖◆❙ ■◆P❯❚ ❋■▲❊ ◆❆▼❊❙❊❚★ ■◆❚❊◆❙■❚❨ ❆❈❈❊P❚❊❉ ❘❊❏❊❈❚❊❉✶ ✵✳✶✽✽✺❊✰✵✸ ✶✼✺✶✸✹ ✵ ✳✳✴❧✶✴❳❉❙❴❆❙❈■■✳❍❑▲✷ ✵✳✷✾✾✻❊✰✵✸ ✷✺✶✵✻ ✵ ✳✳✴❧✷✴❳❉❙❴❆❙❈■■✳❍❑▲

✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲❉❆❚❆ ❙❊❚❙ ◆❯▼❇❊❘ ❖❋ ❈❖▼▼❖◆ ❈❖❘❘❊▲❆❚■❖◆ ❘❆❚■❖ ❖❋ ❈❖▼▼❖◆ ❇✲❋❆❈❚❖❘★✐ ★❥ ❘❊❋▲❊❈❚■❖◆❙ ❇❊❚❲❊❊◆ ✐✱❥ ■◆❚❊◆❙■❚■❊❙ ✭✐✴❥✮ ❇❊❚❲❊❊◆ ✐✱❥

✶ ✷ ✸✹✻✽ ✵✳✾✾✼ ✶✳✵✵✵✵ ✵✳✵✵✵✸✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲

❛ ❜ ■❙❛ ■❙❛✵ ■◆P❯❚ ❉❆❚❆ ❙❊❚✶✳✾✸✻❊✰✵✵ ✹✳✻✺✸❊✲✵✸ ✶✵✳✺✹ ✶✷✳✽✻ ✳✳✴❧✶✴❳❉❙❴❆❙❈■■✳❍❑▲✷✳✽✷✼❊✰✵✵ ✷✳✵✺✼❊✲✵✸ ✶✸✳✶✶ ✶✻✳✾✹ ✳✳✴❧✷✴❳❉❙❴❆❙❈■■✳❍❑▲


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❳❙❈❆▲❊✳▲P

❙❯❇❙❊❚ ❖❋ ■◆❚❊◆❙■❚❨ ❉❆❚❆ ❲■❚❍ ❙■●◆❆▲✴◆❖■❙❊ ❃❂ ✲✸✳✵ ❆❙ ❋❯◆❈❚■❖◆ ❖❋ ❘❊❙❖▲❯❚■❖◆❘❊❙❖▲❯❚■❖◆ ◆❯▼❇❊❘ ❖❋ ❘❊❋▲❊❈❚■❖◆❙ ❈❖▼P▲❊❚❊◆❊❙❙ ❘✲❋❆❈❚❖❘ ❘✲❋❆❈❚❖❘ ❈❖▼P❆❘❊❉ ■✴❙■●▼❆ ❘✲♠❡❛s ❈❈✭✶✴✷✮ ❆♥♦♠❛❧ ❙✐❣❆♥♦ ◆❛♥♦

▲■▼■❚ ❖❇❙❊❘❱❊❉ ❯◆■◗❯❊ P❖❙❙■❇▲❊ ❖❋ ❉❆❚❆ ♦❜s❡r✈❡❞ ❡①♣❡❝t❡❞ ❈♦rr

✼✳✻✵ ✷✺✼✷ ✶✷✵ ✶✷✶ ✾✾✳✷✪ ✺✳✸✪ ✼✳✷✪ ✷✺✼✷ ✹✹✳✹✶ ✺✳✹✪ ✾✾✳✾✯ ✲✻ ✵✳✺✹✸ ✼✻✺✳✸✽ ✹✾✻✾ ✶✾✽ ✶✾✽ ✶✵✵✳✵✪ ✻✳✷✪ ✼✳✻✪ ✹✾✻✾ ✹✺✳✺✷ ✻✳✸✪ ✾✾✳✾✯ ✲✶✺ ✵✳✻✸✼ ✶✺✼✹✳✸✾ ✻✹✽✹ ✷✺✵ ✷✺✵ ✶✵✵✳✵✪ ✻✳✶✪ ✼✳✺✪ ✻✹✽✹ ✹✼✳✹✼ ✻✳✸✪ ✾✾✳✾✯ ✲✷✶ ✵✳✻✾✻ ✷✵✾✸✳✽✵ ✻✼✵✶ ✷✾✸ ✷✾✸ ✶✵✵✳✵✪ ✻✳✾✪ ✼✳✻✪ ✻✼✵✶ ✹✸✳✾✾ ✼✳✵✪ ✾✾✳✾✯ ✶✷ ✵✳✼✾✽ ✷✺✶✸✳✹✵ ✻✼✸✹ ✸✸✶ ✸✸✶ ✶✵✵✳✵✪ ✽✳✶✪ ✽✳✵✪ ✻✼✸✹ ✸✼✳✶✽ ✽✳✸✪ ✾✾✳✽✯ ✾ ✵✳✾✺✻ ✷✽✽✸✳✶✵ ✼✽✽✽ ✸✺✵ ✸✺✵ ✶✵✵✳✵✪ ✽✳✽✪ ✽✳✺✪ ✼✽✽✽ ✸✼✳✼✸ ✾✳✵✪ ✾✾✳✽✯ ✲✸ ✵✳✽✼✵ ✸✶✵✷✳✽✼ ✾✹✷✽ ✹✵✵ ✹✵✵ ✶✵✵✳✵✪ ✶✵✳✺✪ ✾✳✻✪ ✾✹✷✽ ✸✸✳✹✾ ✶✵✳✼✪ ✾✾✳✽✯ ✺ ✵✳✾✷✷ ✸✺✺✷✳✻✾ ✶✵✺✻✹ ✹✷✾ ✹✷✾ ✶✵✵✳✵✪ ✶✷✳✵✪ ✶✶✳✹✪ ✶✵✺✻✹ ✷✾✳✾✶ ✶✷✳✸✪ ✾✾✳✹✯ ✲✶✶ ✵✳✼✽✻ ✸✽✼✷✳✺✸ ✶✵✻✶✺ ✹✶✺ ✹✶✺ ✶✵✵✳✵✪ ✶✸✳✽✪ ✶✸✳✹✪ ✶✵✻✶✺ ✷✻✳✸✸ ✶✹✳✶✪ ✾✾✳✽✯ ✲✶✵ ✵✳✼✽✾ ✸✽✶✷✳✹✵ ✶✷✷✷✾ ✹✼✾ ✹✼✽ ✶✵✵✳✷✪ ✶✺✳✾✪ ✶✺✳✺✪ ✶✷✷✷✾ ✷✸✳✸✺ ✶✻✳✷✪ ✾✾✳✼✯ ✲✶✶ ✵✳✼✾✾ ✹✸✵✷✳✷✾ ✶✷✾✷✸ ✹✾✾ ✺✵✵ ✾✾✳✽✪ ✷✵✳✵✪ ✷✵✳✷✪ ✶✷✾✷✸ ✶✽✳✼✵ ✷✵✳✹✪ ✾✾✳✻✯ ✲✶✵ ✵✳✼✸✼ ✹✺✺✷✳✷✵ ✶✷✼✵✺ ✹✾✵ ✹✾✵ ✶✵✵✳✵✪ ✷✻✳✸✪ ✷✹✳✽✪ ✶✷✼✵✺ ✶✻✳✶✷ ✷✻✳✽✪ ✾✾✳✸✯ ✲✶✵ ✵✳✽✵✸ ✹✺✶✷✳✶✶ ✶✹✹✶✾ ✺✹✾ ✺✹✾ ✶✵✵✳✵✪ ✷✽✳✹✪ ✷✾✳✸✪ ✶✹✹✶✾ ✶✹✳✷✻ ✷✽✳✾✪ ✾✾✳✸✯ ✲✸ ✵✳✼✽✸ ✺✵✼✷✳✵✸ ✶✷✸✺✺ ✺✺✽ ✺✺✽ ✶✵✵✳✵✪ ✸✺✳✺✪ ✸✼✳✻✪ ✶✷✸✺✺ ✶✵✳✹✼ ✸✻✳✹✪ ✾✽✳✸✯ ✲✶ ✵✳✼✻✷ ✺✶✹✶✳✾✻ ✶✵✹✽✼ ✺✼✵ ✺✻✻ ✶✵✵✳✼✪ ✸✽✳✾✪ ✹✶✳✻✪ ✶✵✹✽✼ ✽✳✷✻ ✹✵✳✵✪ ✾✽✳✸✯ ✲✷ ✵✳✼✻✻ ✺✷✽✶✳✾✵ ✶✵✹✾✻ ✺✾✷ ✺✾✻ ✾✾✳✸✪ ✹✽✳✵✪ ✹✾✳✶✪ ✶✵✹✾✻ ✻✳✼✾ ✹✾✳✹✪ ✾✻✳✽✯ ✲✼ ✵✳✼✸✹ ✺✹✾✶✳✽✹ ✶✶✺✹✸ ✻✵✶ ✻✵✶ ✶✵✵✳✵✪ ✻✺✳✽✪ ✼✷✳✷✪ ✶✶✺✹✸ ✹✳✾✸ ✻✼✳✻✪ ✾✺✳✶✯ ✲✼ ✵✳✼✵✻ ✺✻✶✶✳✼✾ ✶✷✸✼✹ ✻✶✻ ✻✶✻ ✶✵✵✳✵✪ ✻✸✳✹✪ ✼✷✳✺✪ ✶✷✸✼✹ ✹✳✾✽ ✻✺✳✵✪ ✾✹✳✾✯ ✲✼ ✵✳✻✻✾ ✺✽✶✶✳✼✹ ✶✷✽✾✶ ✻✸✽ ✻✸✽ ✶✵✵✳✵✪ ✻✻✳✾✪ ✼✽✳✻✪ ✶✷✽✾✶ ✹✳✹✼ ✻✽✳✼✪ ✾✷✳✽✯ ✲✶✵ ✵✳✻✹✹ ✺✾✸✶✳✼✵ ✶✶✽✺✸ ✻✻✽ ✻✼✸ ✾✾✳✸✪ ✽✷✳✶✪ ✶✵✶✳✺✪ ✶✶✽✹✸ ✸✳✵✽ ✽✹✳✺✪ ✽✸✳✷✯ ✲✷✵ ✵✳✻✵✼ ✺✾✼

t♦t❛❧ ✷✵✵✷✸✵ ✾✵✹✻ ✾✵✺✷ ✾✾✳✾✪ ✶✶✳✽✪ ✶✷✳✹✪ ✷✵✵✷✷✵ ✶✽✳✵✽ ✶✷✳✵✪ ✾✾✳✾✯ ✲✻ ✵✳✼✹✾ ✽✶✽✵


ACSA

Parameter Refinement


ACSA

❘❊❋■◆❊-ment of Parameters

• Refinement occurs at three stages:

1. ❘❊❋■◆❊✭■❉❳❘❊❋✮: Initial parameter (Distance, beam, cell. . . )

2. ❘❊❋■◆❊✭■◆❚❊●❘❆❚❊✮: Refinement of parameters per wedge of data (❉❊▲P❍■ ❂ ✺✳✵: macromolecular cell

(default); ❉❊▲P❍■ ❂ ✸✵✳✵: small cell)

3. ❈❖❘❘❊❈❚: Global refinement

• ❂❇❊❆▼ ❆❳■❙ ❖❘■❊◆❚❆❚■❖◆ ❈❊▲▲ ❉■❙❚❆◆❈❊

Default: all; reasonable setting:

❘❊❋■◆❊✭■❉❳❘❊❋✮❂❇❊❆▼ ❆❳■❙ ❖❘■❊◆❚❆❚■❖◆ ❈❊▲▲ ✦❉■❙❚❆◆❈❊

❘❊❋■◆❊✭■◆❚❊●❘❆❚❊✮❂✦❉■❙❚❆◆❈❊ ❇❊❆▼ ❖❘■❊◆❚❆❚■❖◆ ❈❊▲▲ ✦❆❳■❙

✦❘❊❋■◆❊✭❈❖❘❘❊❈❚✮❂❉■❙❚❆◆❈❊ ❇❊❆▼ ❖❘■❊◆❚❆❚■❖◆ ❈❊▲▲ ❆❳■❙


ACSA

Parameter Refinement

IDXREF

COLSPOT

INIT

XYCORR

CORRECT

INTEGRATE

DEFPIX

Step

SPOT.XDS

XPARM.XDS

INTEGRATE.HKL

input files

SPOT.XDS

XPARM.XDS

FRAME.cbf

SPOT.XDS

ABS.cbf

BKGPIX.cbf

FRAME.cbf

INTEGRATE.HKL

XDS_ASCII.HKL

GXPARM.XDS

output files

(Important)

• ❈❖❘❘❊❈❚ globally refines the parameters

(❘❊❋■◆❊✭❈❖❘❘❊❈❚✮❂✳✳✳ based on all reflections

• ♠✈ ●❳P❆❘▼✳❳❉❙ ❳P❆❘▼✳❳❉❙

• ①❞s ♣❛r

• Do not run IDXREF: overwrite XPARM.XDS:

❏❖❇ ❂ ❉❊❋P■❳ ■◆❚❊●❘❆❚❊ ❈❖❘❘❊❈❚

• Automatic Laue group assignment unless

❙P❆❈❊ ●❘❖❯P ◆❯▼❇❊❘ present in ❳❉❙✳■◆P


ACSA

■❉❳❘❊❋: Indexing


ACSA


1. Input: strong spots found in ❈❖▲❙P❖❚ step

2. Saving time: Run COLSPOT on entire data set, select images for indexing with (multiple) ❙P❖❚ ❘❆◆●❊❂ ✳✳✳.

Rerun ■❉❳❘❊❋, but not ❈❖▲❙P❖❚ when there are difficulties.


ACSA


• Indexing step: Find cell parameters and cell orientation.

• First refinement of experimental parameters (Detector distance, . . . )

• Writes solution to ❳P❆❘▼✳❳❉❙

❳P❆❘▼✳❳❉❙ ❱❊❘❙■❖◆ ▼❛r❝❤ ✸✵✱ ✷✵✶✸✶ ✵✳✵✵✵✵ ✵✳✶✵✵✵ ✵✳✵✵✶✷✻✸ ✲✵✳✾✾✾✾✾✽ ✲✵✳✵✵✶✺✾✶✵✳✾✼✻✷✻✵ ✵✳✵✵✵✼✵✶ ✲✵✳✵✵✵✾✹✷ ✶✳✵✷✹✸✶✼

✶ ✶✷✷✳✽✵✹✺ ✶✹✵✳✶✺✽✼ ✷✶✶✳✽✹✻✹ ✶✵✾✳✸✵✾ ✾✾✳✺✽✸ ✾✵✳✵✶✷ ❁✲✲✲ ❈❡❧❧✲✹✳✻✵✸✶✶✾ ✽✼✳✶✾✺✸✵✺ ✲✽✻✳✸✺✷✷✾✺✲✽✳✷✽✾✼✼✺ ✾✽✳✷✵✾✽✸✶ ✾✾✳✻✺✷✷✻✼✷✵✶✳✼✼✹✾✾✹ ✲✻✵✳✼✶✷✶✺✹ ✲✷✶✳✾✵✹✸✹✸

✶ ✷✹✻✸ ✷✺✷✼ ✵✳✶✼✷✵✵✵ ✵✳✶✼✷✵✵✵✶✷✸✶✳✼✸✹✷✺✸ ✶✷✻✺✳✼✺✸✺✹✵ ✻✷✵✳✾✻✹✻✵✵ ❁✲✲✲ ❉✐st❛♥❝❡

✶✳✵✵✵✵✵✵ ✵✳✵✵✵✵✵✵ ✵✳✵✵✵✵✵✵✵✳✵✵✵✵✵✵ ✶✳✵✵✵✵✵✵ ✵✳✵✵✵✵✵✵✵✳✵✵✵✵✵✵ ✵✳✵✵✵✵✵✵ ✶✳✵✵✵✵✵✵✶ ✶ ✷✹✻✸ ✶ ✷✺✷✼

✵✳✵✵ ✵✳✵✵ ✵✳✵✵ ✶✳✵✵✵✵✵ ✵✳✵✵✵✵✵ ✵✳✵✵✵✵✵ ✵✳✵✵✵✵✵ ✶✳✵✵✵✵✵ ✵✳✵✵✵✵✵


ACSA

❙P❖❚✳❳❉❙

• ❈❖▲❙P❖❚: Detector coordinates and Intensity of strong spots to be used for indexing:

❳✭♣✐①❡❧✮ ❨✭♣✐①❡❧✮ ★✐♠❛❣❡ ❝♦✉♥ts

✶✵✺✻✳✶✶ ✶✺✷✾✳✺✶ ✶✺✳✸✺ ✷✺✹✹✳

✶✽✾✺✳✺✷ ✶✺✷✺✳✹✾ ✾✳✶✾ ✷✹✽✶✳

✶✾✶✸✳✹✸ ✶✺✹✼✳✾✵ ✷✳✻✸ ✶✾✾✾✳

• ■❉❳❘❊❋: Miller-Indices according to ❳P❆❘▼✳❳❉❙

❳✭♣✐①❡❧✮ ❨✭♣✐①❡❧✮ ★✐♠❛❣❡ ❝♦✉♥ts ❍ ❑ ▲

✶✵✺✻✳✶✶ ✶✺✷✾✳✺✶ ✶✺✳✸✺ ✷✺✹✹✳ ✶✹ ✶✸ ✶✽

✶✽✾✺✳✺✷ ✶✺✷✺✳✹✾ ✾✳✶✾ ✷✹✽✶✳ ✲✼ ✲✶✸ ✲✶✹

✶✾✶✸✳✹✸ ✶✺✹✼✳✾✵ ✷✳✻✸ ✶✾✾✾✳ ✵ ✵ ✵ ❁✲✲✲

• ✵ ✵ ✵: not indexed with current cell


ACSA

Failed Indexing

XDS stops if less than 50 % of all reflections in SPOT.XDS could be indexed.

✯✯✯✯✯ ■◆❉❊❳■◆● ❖❋ ❖❇❙❊❘❱❊❉ ❙P❖❚❙ ■◆ ❙P❆❈❊ ●❘❖❯P ★ ✶ ✯✯✯✯✯✷✼✾ ❖❯❚ ❖❋ ✾✵✷✸ ❙P❖❚❙ ■◆❉❊❳❊❉✳✵ ❘❊❏❊❈❚❊❉ ❘❊❋▲❊❈❚■❖◆❙ ✭❘❊❆❙❖◆✿ ❖❱❊❘▲❆P✮

✽✼✹✹ ❘❊❏❊❈❚❊❉ ❘❊❋▲❊❈❚■❖◆❙ ✭❘❊❆❙❖◆✿ ❚❖❖ ❋❆❘ ❋❘❖▼ ■❉❊❆▲ P❖❙■❚■❖◆✮

• Refined distance reasonable?

• Cell reasonable?

❯◆■❚ ❈❊▲▲ P❆❘❆▼❊❚❊❘❙ ✶✵✳✾✵✻ ✶✺✳✻✹✶ ✷✺✳✶✺✺ ✼✽✳✷✽✾ ✾✵✳✾✺✼ ✼✵✳✸✼✷❈❘❨❙❚❆▲ ❚❖ ❉❊❚❊❈❚❖❘ ❉■❙❚❆◆❈❊ ✭♠♠✮ ✶✼✶✳✶✻ ✦ ❁✲✲✲ ❤❡❛❞❡r✿ ✶✼✵✳✵✵♠♠


ACSA

Example: Difficult Case

✷✾✺✶ ❖❯❚ ❖❋ ✶✺✺✵✼ ❙P❖❚❙ ■◆❉❊❳❊❉✳

✵ ❘❊❏❊❈❚❊❉ ❘❊❋▲❊❈❚■❖◆❙ ✭❘❊❆❙❖◆✿ ❖❱❊❘▲❆P✮

✶✷✺✺✻ ❘❊❏❊❈❚❊❉ ❘❊❋▲❊❈❚■❖◆❙ ✭❘❊❆❙❖◆✿ ❚❖❖ ❋❆❘ ❋❘❖▼ ■❉❊❆▲ P❖❙■❚■❖◆✮


ACSA

“Manual Indexing” with ❛❞①✈ [3]

❯◆■❚ ❈❊▲▲ P❆❘❆▼❊❚❊❘❙ ✶✵✳✾✵✻ ✶✺✳✻✹✶ ✷✺✳✶✺✺ ✼✽✳✷✽✾ ✾✵✳✾✺✼ ✼✵✳✸✼✷

⇒ ❏❖❇ ❂ ❉❊❋P■❳ ■◆❚❊●❘❆❚❊ ❈❖❘❘❊❈❚: integrate with this solution


ACSA

Twinning / Multiple Lattices: Search for Extra Lattices

Patient? use s♣♦ts✹❝❡❧❧♥♦✇ and ❝❡❧❧ ♥♦✇

Impatient?

1. create new directory ★❃ ♠❦❞✐r ❧❛tt✷

2. ★❃ ❣r❡♣ ✧✵ ✵ ✵ ✧ ❙P❖❚✳❳❉❙ ❃ ❧❛tt✷✴❙P❖❚✳❳❉❙

3. rerun ❏❖❇❂■❉❳❘❊❋

4. compare orientations in ❳P❆❘▼✳❳❉❙

5. integrate each lattice separately

Caveat: ❳❉❙ is not set up to integrate overlapping spots


ACSA

Example: Insulin Crystal with a Satellite

~a = (73.15,−24.82,−14.45)

~b = (10.46,59.86,−49.83)

~c = (26.74,44.46,59.02)

~a = (72.17,−27.40,−16.02)

~b = (30.84,51.13,51.48)

~c = (−7.50,−53.39,57.53)


ACSA

Study Case I: SPAnH (R. Herbst-Irmer)

• Question: Are observed differences between Fobs and Fcalc s❛✐♥t–specific?

• 5 runs @ 2θ = 30◦

• 5 runs @ 2θ = 78◦

• data converted from s❢r♠ to ▼❛r❈❈❉ format


ACSA

Setting up ❳❉❙✳■◆P for ✳s❢r♠-format

Difficulty: transfer collection geometry to XDS input description.

❙❛✐♥t Coordinate System ❳❉❙ Coordinate System

❫✰❩▲

⑤ ✴

⑤✴

✰❳▲ ❁❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂ ❙♦✉r❝❡

✴ ⑤

✴ ⑤

✰❨▲ ⑤

⑤

❫

⑤ ✴ ✰❳▲

⑤✴

✰❩▲ ❁❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂❂ ❙♦✉r❝❡

✴ ⑤

✴ ⑤

⑤

✈ ✰❨▲

Non-perpendicular axes: rotation axis 6= (−100) or (0− 10) . . .

SPAnH: only ω–scans: rotation axis = (0− 10)


ACSA

s❢r♠t♦♦❧s

★❃ s❢r♠t♦♦❧s ❧✐❞✶❴❝✷✲✷❴✵✼❴✵✵✵✶✳s❢r♠

✦ ✷t❤❡t❛ ❂ ✶✺❞❡❣✱ ❛ss✉♠✐♥❣ ✈❡rt✐❝❛❧ s✇✐♥❣ ❛①✐s

❉■❘❊❈❚■❖◆❴❖❋❴❉❊❚❊❈❚❖❘❴❳✲❆❳■❙❂ ✵✳✾✻✺✾✷✻ ✵✳✵ ✵✳✷✺✽✽✶✾

❉■❘❊❈❚■❖◆❴❖❋❴❉❊❚❊❈❚❖❘❴❨✲❆❳■❙❂ ✵✳✵ ✶✳✵ ✵✳✵

❳✲❘❆❨❴❲❆❱❊▲❊◆●❚❍❂✶✳✺✹✶✽✽✹ ✦❆♥❣str♦❡♠

❖❙❈■▲▲❆❚■❖◆❴❘❆◆●❊❂ ✵✳✶✼✾✾✾✸

❖❘●❳❂ ✺✵✺✳✼✸✵✵✶✶ ❖❘●❨❂ ✺✶✸✳✹✹✵✵✵✷

❉❊❚❊❈❚❖❘❴❉■❙❚❆◆❈❊❂ ✺✵✳✵✵✵✵✵✵ ✦✭♠♠✮

❉❆❚❆❴❘❆◆●❊❂ ✶ ✷✵✵✵

✦ ❘♦t❛t✐♦♥ ❛❜♦✉t ♣❤✐ ❛①✐s

❘❖❚❆❚■❖◆❴❆❳■❙❂ ✵✳✼✽✾✷✻✷ ✲✵✳✺✼✻✹✽✾ ✵✳✷✶✶✹✽✷

Append to XDS.INP

❳❉❙ does not read sfrm (missing spatial correction) ⇒ export to ♠❛r❝❝❞ within ❆P❊❳


ACSA

Unstable Refinement

• Small Cell = few spots within ≈ 5◦

• Leads to unstable parameter refinement in ■◆❚❊●❘❆❚❊

• Solution then: Increase ❉❊▲P❍■❂✹✵ (20-60)

• Better: Ensure correct orientation after indexing and set

❘❊❋■◆❊✭■◆❚❊●❘❆❚❊✮❂✦

✦❘❊❋■◆❊✭❈❖❘❘❊❈❚✮❂✳✳✳

⇒ no refinement during integration, global refinement of all parameters with all reflections

• Caveat: Check ❋❘❆▼❊✳❝❜❢ — XDS can loose orientation and spots


ACSA

Some Statistics for SPAnH

❘❡s♦❧✉t✐♦♥ ★❉❛t❛ ★❚❤❡♦r② ✪❈♦♠♣❧❡t❡ ❘❡❞✉♥❞❛♥❝② ▼❡❛♥ ■ ▼❡❛♥ ■✴s ❘♠❡r❣❡ ❘s✐❣♠❛■♥❢ ✲ ✶✳✽✸ ✻✺✵ ✻✼✺ ✾✻✳✸ ✹✳✻✵ ✷✾✶✳✹ ✺✶✳✺✾ ✵✳✵✶✾✻ ✵✳✵✶✼✶

✶✳✽✸ ✲ ✶✳✷✸ ✶✺✺✷ ✶✺✺✷ ✶✵✵✳✵ ✹✳✺✾ ✶✺✵✳✵ ✹✵✳✻✷ ✵✳✵✷✷✾ ✵✳✵✶✼✽✶✳✷✸ ✲ ✵✳✾✽ ✷✶✻✼ ✷✶✻✼ ✶✵✵✳✵ ✸✳✼✽ ✾✸✳✹ ✷✾✳✸✻ ✵✳✵✷✾✺ ✵✳✵✷✸✸✵✳✾✽ ✲ ✵✳✽✻ ✷✶✵✽ ✷✶✵✽ ✶✵✵✳✵ ✸✳✾✽ ✻✻✳✺ ✷✾✳✼✸ ✵✳✵✸✹✽ ✵✳✵✷✹✻✵✳✽✻ ✲ ✵✳✼✽ ✷✷✵✹ ✷✷✵✻ ✾✾✳✾ ✹✳✽✵ ✹✽✳✵ ✸✺✳✶✽ ✵✳✵✸✽✹ ✵✳✵✷✵✵✵✳✼✽ ✲ ✵✳✼✷ ✷✸✻✶ ✷✸✼✽ ✾✾✳✸ ✹✳✹✼ ✸✾✳✸ ✸✶✳✷✼ ✵✳✵✹✺✵ ✵✳✵✷✷✽✵✳✼✷ ✲ ✵✳✻✽ ✷✵✶✽ ✷✵✼✹ ✾✼✳✸ ✸✳✼✽ ✷✾✳✽ ✷✻✳✾✷ ✵✳✵✺✵✻ ✵✳✵✷✻✷✵✳✻✽ ✲ ✵✳✻✹ ✷✹✽✽ ✷✻✵✺ ✾✺✳✺ ✶✳✾✺ ✷✻✳✼ ✷✸✳✸✹ ✵✳✵✷✼✼ ✵✳✵✸✵✶✵✳✻✹ ✲ ✵✳✻✶ ✷✸✸✺ ✷✹✻✼ ✾✹✳✻ ✶✳✼✷ ✷✷✳✼ ✷✶✳✷✷ ✵✳✵✷✹✽ ✵✳✵✸✸✷✵✳✻✶ ✲ ✵✳✺✾ ✶✼✾✶ ✶✾✶✷ ✾✸✳✼ ✶✳✻✼ ✶✾✳✽ ✶✾✳✺✼ ✵✳✵✷✽✻ ✵✳✵✸✺✼✵✳✺✾ ✲ ✵✳✺✼ ✷✵✸✽ ✷✷✵✵ ✾✷✳✻ ✶✳✻✷ ✶✻✳✸ ✶✼✳✻✵ ✵✳✵✸✷✽ ✵✳✵✹✵✵✵✳✺✼ ✲ ✵✳✺✺ ✷✸✷✷ ✷✺✸✷ ✾✶✳✼ ✶✳✺✽ ✶✷✳✼ ✶✺✳✾✵ ✵✳✵✸✽✶ ✵✳✵✹✺✼✵✳✺✺ ✲ ✵✳✺✸ ✷✻✸✵ ✷✾✵✶ ✾✵✳✼ ✶✳✺✷ ✾✳✺ ✶✸✳✸✾ ✵✳✵✹✹✷ ✵✳✵✺✺✵✵✳✺✸ ✲ ✵✳✺✷ ✶✹✻✹ ✶✻✸✷ ✽✾✳✼ ✶✳✹✽ ✼✳✷ ✶✶✳✹✹ ✵✳✵✹✾✺ ✵✳✵✻✺✽✵✳✺✷ ✲ ✵✳✺✵ ✸✷✹✾ ✸✻✾✹ ✽✽✳✵ ✶✳✹✶ ✺✳✽ ✶✵✳✵✾ ✵✳✵✹✾✺ ✵✳✵✼✻✸✵✳✺✵ ✲ ✵✳✹✾ ✶✼✽✹ ✷✵✹✷ ✽✼✳✹ ✶✳✸✼ ✺✳✵ ✾✳✸✽ ✵✳✵✺✻✻ ✵✳✵✽✹✹✵✳✹✾ ✲ ✵✳✹✽ ✶✾✻✺ ✷✷✽✶ ✽✻✳✶ ✶✳✸✸ ✹✳✺ ✽✳✺✾ ✵✳✵✺✽✶ ✵✳✵✾✶✸✵✳✹✽ ✲ ✵✳✹✼ ✷✵✹✸ ✷✹✶✸ ✽✹✳✼ ✶✳✷✼ ✹✳✺ ✽✳✼✸ ✵✳✵✺✻✷ ✵✳✵✾✶✼✵✳✹✼ ✲ ✵✳✹✻ ✷✷✵✵ ✷✻✺✾ ✽✷✳✼ ✶✳✷✸ ✹✳✹ ✽✳✹✻ ✵✳✵✻✸✵ ✵✳✵✾✹✶✵✳✹✻ ✲ ✵✳✹✺ ✷✸✽✶ ✷✾✶✼ ✽✶✳✻ ✶✳✶✽ ✹✳✷ ✽✳✷✶ ✵✳✵✺✾✼ ✵✳✵✾✼✵✵✳✹✺ ✲ ✵✳✹✹ ✶✷✹✼ ✶✽✵✹ ✻✾✳✶ ✵✳✾✺ ✸✳✽ ✼✳✻✶ ✵✳✵✻✽✸ ✵✳✶✵✻✹✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✲✵✳✺✹ ✲ ✵✳✹✹ ✶✼✻✾✸ ✷✵✾✹✾ ✽✹✳✺ ✶✳✸✵ ✺✳✷ ✾✳✸✾ ✵✳✵✺✸✺ ✵✳✵✽✷✷■♥❢ ✲ ✵✳✹✹ ✹✷✾✾✼ ✹✼✷✶✾ ✾✶✳✶ ✷✳✷✸ ✸✶✳✸ ✶✾✳✷✺ ✵✳✵✸✵✽ ✵✳✵✷✼✼

▼❡r❣❡❞ ❬❆❪✱ ❧♦✇❡st r❡s♦❧✉t✐♦♥ ❂ ✶✻✳✾✶ ❆♥❣str♦♠s

❘❊▼ ❤❡❧✐❴r✉♥s✶✲✺❴❤✐❣❤✶✲✹ ✐♥ P✲✶❘❊▼ ✶✵✳✷✷ ✶✷✳✷✽ ✶✼✳✸✹ ✶✵✶✳✺✼✼ ✾✶✳✷✻✼ ✶✶✷✳✵✹✺❘❊▼ ❘✶ ❂ ✵✳✵✹✶✸ ❢♦r ✸✺✷✶✺ ❋♦ ❃ ✹s✐❣✭❋♦✮ ❛♥❞ ✵✳✵✺✵✾ ❢♦r ❛❧❧ ✹✷✾✾✼ ❞❛t❛❘❊▼ ✻✺✼ ♣❛r❛♠❡t❡rs r❡❢✐♥❡❞ ✉s✐♥❣ ✵ r❡str❛✐♥ts


ACSA

Study Case II: Peroxo (K. Dalle, AK Meyer)

• Cell: ✶✵✳✾ ✶✷✳✽ ✶✼✳✻ ✼✷✳✼ ✽✵✳✸ ✽✺✳✻

• Disorder

• Multiple lattices

• Five crystals +κ Goniometer at BL14.1 (BESSY):

• 10 Data sets collected, 199GB data, 34283 frames


ACSA

XDS: Mosaicity and Beam Divergence

Two Parameters control the size of spots on the detector:

✦❇❊❆▼❴❉■❱❊❘●❊◆❈❊❂ ✵✳✽✵ ✦❛r❝t❛♥✭s♣♦t ❞✐❛♠❡t❡r✴❉❊❚❊❈❚❖❘❴❉■❙❚❆◆❈❊✮

✦❇❊❆▼❴❉■❱❊❘●❊◆❈❊❴❊✳❙✳❉✳❂ ✵✳✵✽✵ ✦❤❛❧❢✲✇✐❞t❤ ✭❙✐❣♠❛✮ ♦❢ ❇❊❆▼❴❉■❱❊❘●❊◆❈❊

✦❘❊❋▲❊❈❚■◆●❴❘❆◆●❊❂ ✵✳✼✽✵ ✦❢♦r ❝r♦ss✐♥❣ t❤❡ ❊✇❛❧❞ s♣❤❡r❡ ♦♥ s❤♦rt❡st r♦✉t❡

✦❘❊❋▲❊❈❚■◆●❴❘❆◆●❊❴❊✳❙✳❉✳❂ ✵✳✶✶✸ ✦❤❛❧❢✲✇✐❞t❤ ✭♠♦s❛✐❝✐t②✮ ♦❢ ❘❊❋▲❊❈❚■◆●❴❘❆◆●❊

If undefined: adjusted by ❳❉❙ during ■◆❚❊●❘❆❚❊ step

Profiles shown in ■◆❚❊●❘❆❚❊✳▲P — search for "❘❯◆✲❆❱❊❘❆●❊"


ACSA

Undefined Mosaicity and Beam Divergence

• Combination of Spots

• Wrong Intensities ⇒ large R-values

• Wrong Spot Positions: Wrong Pa-

rameter Refinement

• Jump between two lattices


ACSA

Mosaicity and Beam Divergence too Small

• Wrong Intensities ⇒ large R-values

• Inbetween two lattices: “zero” inten-

sity


ACSA

Mosaicity and Beam Divergence adjusted


ACSA

Peroxo: Some Results

One crystal, four κ settings: 0◦,10◦,20◦,30◦

❘❊▼ ▲✐❞✶❴❈✷❴❛❧❧ ✐♥ P✲✶

❘❊▼ ❘✶ ❂ ✵✳✵✻✽✾ ❢♦r ✻✺✹✶ ❋♦ ❃ ✹s✐❣✭❋♦✮ ❛♥❞ ✵✳✵✼✵✵ ❢♦r ❛❧❧ ✻✼✶✵ ❞❛t❛

❘❊▼ ✼✻✸ ♣❛r❛♠❡t❡rs r❡❢✐♥❡❞ ✉s✐♥❣ ✾✵✾ r❡str❛✐♥ts


ACSA

References

1. Leslie, A.G.W., Recent changes to the MOSFLM package for processing film and image plate data,

Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography (1992), No. 26

2. A.N. Popov and Bourenkov , Choice of data-collection parameters based on statistic modeling Acta

Crystallogr. (2003). D59, 1145-1153

3. Andrew Arvai, http://www.scripps.edu/˜arvai/adxv.html


http://www.scripps.edu/~arvai/adxv.html

advanced crystal structure analysis using xds with small...

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