SADABS User Manual
Contents
1. diffracted beam If absorption is small we recommend the default values of 4 and 1 for moderate absorption 6 and 3 are suitable and for strong absorption 8 and 5 Theoretically the odd order can be lower if the crystal shape is centrosymmetric For higher orders the program will be significantly slower Now the program asks if special treatment of a thin plate crystal is required If the answer is Y the indices of the prominent face are requested The Bruker CCD microscope attachment and software are well able to determine these indices but if you have accidentally forgotten to measure them you can use SADABS to find them by trial and error The indices are usually small numbers such as 0 0 1 and if unsuitable values are used the value of u t u is the linear absorption coefficient t is the thickness simply refines asymptotically to zero The minimum glancing angle enables reflections for which either the incident or the diffracted beam glances the plate to be ignored for the purposes of parameter refinement a different value may be specified later for correction of all the data These reflections suffer from large and uncertain absorption corrections The absorption is also affected by slight bending of the plate and by the beam divergence so it is better to leave such reflections out with luck equivalents that do not suffer from this problem will be present in the data set Trying the correction with and without2. know the Laue group either from SMART or in tricky cases by preliminary examination of a raw file with XPREP without correction using SADABS and you should have prepared either a single merged data file m raw or one raw file for each scan using SAINT All the raw files must be from the same crystal indexed consistently i e the orientation matrices should be similar but not necessarily identical Data from more than one crystal should be processed separately with SADABS and merged using XPREP If data were inadvertently indexed inconsistently for different scans or in a way that does not correspond to the conventional setting of the Laue group the T option in the D submenu in XPREP may be used to transform the indices and direction cosines Note that SADABS can now read the merged raw file not possible in previous versions and we strongly recommend that you set the instrument error factor to O when processing the data with SAINT A non zero value can make it impossible for SADABS to find a good error model SADABS now detects the use of a wrong value for the instrument error and offers to try to repair the damage done useful for reading old raw files for which the frames have been lost 2 1 Input of Data and Modeling of Absorption and Other Systematic Errors On starting SADABS the first question asks for the name of a file used for a protocol of the SADABS run You should give a name that identifies the cr
3. output by SAINT The best test of success in establishing a good error model is that the Postscript plots of y against intensity and against resolution should be horizontal lines with x equal to one After establishing the weighting scheme the program prints a table giving for each scan the following information Rin minimum and maximum values for the incident and diffracted beam transmission factors k see above the number of reflections and the number with intensity greater than 2su At this stage it is again possible to repeat the parameter refinement or the determination of the error model We must emphasize that the Rin value although traditional is a very poor guide to the quality of the data It is very easy to reduce it artificially by overfitting the data e g by making the scale factor restraint esd larger or by using high order spherical harmonics when there is no absorption or by rejecting too many reflections Diederichs amp Karplus Nature Struct Biol 4 1997 269 275 The final R1 value bond length and angle standard uncertainties and largest peak and hole in the difference electron density map after refinement are a much better guide provided the same number of reflections are compared And x values of unity over the full resolution and intensity range are also a good indication that the processed data are free from serious systematic errors 2 3 Output of Postscript Diagnostic Plots and C
4. the special thin plate treatment is always worthwhile In many cases the general spherical harmonic treatment with orders 8 and 5 is just as good and converges significantly faster The program then enters the parameter refinement If a plate like crystal was specified the default number of cycles is 20 otherwise it is 10 We are still trying to speed up the convergence of the thin plate correction Each refinement cycle consists of two subcycles In the first the scale factors S n one for each frame restrained as discussed above are refined together with three extra parameters for thin plates In the second the diffracted beam absorption P u v w is modeled using spherical harmonic functions of the orthogonalized diffracted beam direction cosines u v and w Blessing Acta Cryst A51 1995 33 38 L I S n P u v w The frame number n is non integral the centroid of a reflection will fall between two frames so a linear interpolation is required x n N Ninteger 0 lt x lt 1 S n 1 x Sy x Sy 1 Including the restraints with esds e after conversion from fractional to absolute values for adjacent scale factors the quantity minimized is Z w lt L gt 1 X Sy Swsi 7 where lt I gt is the mean corrected intensity of a group of equivalent reflections The values of Rin are printed after each half cycle for the reflections used for parameter determination only If the thin plate correc
5. BRUKER ADVANCED X RAY SOLUTIONS G UKER SADABS User Manual Area Detector Absorption and Other Corrections Version 2 03 Purpose These instructions cover operation of the SADABS program Responsibilities All procedures are to be performed by general users site administrators and trained Bruker AXS personnel Disclaimer All configurations and specifications are subject to change without notice 1 Introduction The SADABS program is designed to exploit data redundancy to correct 3D integrated thin slice data from Bruker CCD and MWPC area detectors SADABS provides useful diagnostics and can correct for errors such as variation in the volume of the crystal irradiated incident beam inhomogeneity absorption by the crystal support e g when the goniometer head passes under the collimator during an omega scan on a Bruker PLATFORM goniometer and crystal decay The program also improves the esds of the intensities so we strongly recommend that you use it to process ALL data whether or not absorption is significant These corrections also enable larger crystals to be used for weakly diffracting crystals without introducing systematic errors For an impressive example see C H G rbitz Acta Cryst B55 1999 1090 1098 SADABS reads the raw files generated by the Bruker AXS integration program SAINT No other files environment variables etc are required SADABS is currently available as a stand alone exe
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7. cutable for the following operating M86 E00046 0102 systems Windows 95 Windows 98 Windows NT Windows 2000 IRIX 6 5 and Linux Intel 2 Startup Note This procedure assumes the software has been properly installed You start the program by clicking on SADABS from the SAINT main menu You may also start the program from a command line in an MS DOS window under Windows with the command sadabs or in the case of Windows by double clicking on a program icon in which case a temporary dialog window opens The executable must be in a directory that is in the current PATH under Linux this could be usr local bin Note that under Windows the PATH may be set in a batch file that is called when an MS DOS window is opened User interaction with SADABS is by means of question and answer You should answer almost all questions with ENTER to accept the defaults suggested by the program unless you have a very good reason not to The action of the program is divided into three sections e Input of data and modeling of absorption and other systematic errors e Error analysis and derivation of correct standard uncertainties for the corrected intensities e Output of Postscript diagnostic plots and corrected data This manual follows the order of a typical SADABS session so it is a good idea to refer to the manual while running SADABS until you are familiar with the program Before running SADABS you will need to
8. d the Rin value for the reflections used for parameter refinement is printed This value is usually lower than the Rint value for all the data determined by XPREP especially if a large number of weak data were not used for parameter determination The program then asks if the parameter refinement should be repeated with new settings or not This repeating is useful if you are investigating possible thin plate indices but usually a better M86 E00046 0102 practice is to complete the error model analysis and look at the Postscript plots before repeating the optimization of the absorption etc model 2 2 Error Analysis and Derivation of Correct Standard Uncertainties for the Corrected Intensities The next stage Part 2 of the program is the determination of an error model First it is necessary to specify which reflections should be considered to be erroneous and left out for the purposes of defining the correct o I values and preparing the diagnostic plots and from the final output file of corrected intensities A resolution limit possibly different from that used for parameter determination should be specified In the case of a thin plate correction a glancing angle test may also be applied which may also be different from the limit used for parameter determination Then an error o l limit may be applied default 4 00 The idea is to eliminate reflection measurements suffering from serious systematic errors e
9. e crystal quality and on the characteristics of the individual detector employed so we advise you to refine it rather than use a fixed value The next question asks for the restraint esd for consecutive scale factors expressed as a fraction of their values This should almost always be in the range 0 001 to 0 005 and the default of 0 002 is a good first try The best value to use depends on the number of reflections per frame and the redundancy and quality of the data so guessing in advance is difficult The best guide is the appearance of the Postscript plot of the incident beam correction this correction should be smooth but still show a slight amount of high frequency noise lf the value is too small the correction may be over restrained and the merging R values Rint will be appreciably higher if the value is too large the plot will be noisy and the data may be over fitted leading to artificially low merging R values In general the R1 value at the end of the structure refinement will show a shallow minimum as a function of the value of this restraint In critical cases you can use this test to obtain the optimum value The original version of SADABS used Savitsky Golay smoothing instead of restraints but restraints are more flexible and can better handle the case of a very small number of reflections per frame The program then asks for the highest orders to be used for the spherical harmonic absorption correction of the
10. e values indicate that something is seriously wrong and that the data integration with SAINT should be investigated and possibly repeated The program also estimates the maximum 2theta and wavelength from the direction cosines and other information in the raw file These estimates are output only as a rough check on the consistency of the direction cosines etc They suffer from rounding errors and so should not be treated as definitive Having input the data successfully the program starts with Part 1 the determination of a model for the systematic errors You can return to this point later to repeat the remaining calculations without having to read the data in again The program prints out the total number of reflections and the number that are unique this number depends on the Laue group and the treatment of Friedel opposites followed by an analysis of redundancy and mean l a 1 The program then asks for the mean l c 1 threshold for including a group of equivalents in the subset of reflections used for parameter refinement If the data were processed with a modern version of SAINT the default value of 3 will usually be good If the data are exceptionally weak evident from the statistics that immediately precede the question a value of 2 5 or even 2 0 could be tried If the data were processed with an old version of SAINT that tended to underestimate the o l values you might be better off entering 5 here The next ques
11. g a reflection cut off by the beam stop or close to a strong reflection from an ice crystal or other impurity not to throw out a large number of reflections in order to reduce the merging R values If the data conform to a normal distribution and the weights are correct 0 27 will deviate by more than 30 and 0 05 by more than 3 50 Fewer than 0 01 should deviate more than 4 00 Since these statistics assume purely random errors and some systematic errors inevitably remain these numbers represent lower limits on the percentages of outliers that should be retained in the data to avoid violating the statistical treatment In practice a cutoff of about 4 00 catches the real errors without upsetting the statistics too much The program prints out the total number of data and the number of unique data before and after applying these rejection tests and you are given the opportunity to experiment with different cutoff values Note the logic of applying this rejection threshold after modeling absorption and other errors rather than before as would be the case using the Filter option in SAINT M86 E00046 0102 After you have decided which reflections to ignore SADABS tries to find the best g value for the error model sul k O I 8 lt 1 gt Y where k is a scaling factor and su l is the corrected standard uncertainty of the corrected intensity I and o l o 1 S n P u v w where o I is the esd of the intensity
12. nged we recommend that each system be calibrated The best plan is to find a strongly scattering crystal in a space group with many systematic absences e g Pbca a centered lattice can also be used provided that SAINT is told that it is primitive but this puts a strain on the integration and try various values of the 1 2 factor so that the mean I o l for the systematic absences output by XPREP is about unity or slightly less This correction has virtually no affect on the reflections that should not have zero intensity but you may want to apply it so that the systematic M86 E00046 0102 absences can be recognized and the space group assigned correctly The program allows you to leave out or reinstate particular scans without having to read the data in again and start again with the determination of the parameters to model systematic errors The table at the end of Part 2 may indicate that a particular scan is much worse than the others in which case you can try again leaving it out Finally you may end the SADABS run with Q BORE ISO 9001 APPROVAL gt a A m o m o Conditions for use of this mark are controlled by AOQC Moody International Inc USA BRUKER AXS INC 5465 EAST CHERYL PARKWAY MADISON WI 53711 5373 USA TEL 1 800 234 XRAY TEL 1 608 276 3000 FAX 1 608 276 3006 Email info Obruker axs com http www bruker axs com BRUKER AXS GMBH D 76181 KARLSRUHE G
13. nslational symmetry A systematic drop or rise at high resolution may indicate problems with the SAINT integration e g integrating data that were not present Macromolecules may show solvent artifacts at low resolution but should otherwise fall fairly closely to the non centrosymmetric line For inorganic structures with heavy atoms on special positions this plot is less reliable The third page shows the distribution of x as a function of resolution and intensity The closer these two plots are to a horizontal line at x equal to one the better the fit to the error model and the more reliable the standard uncertainties of the corrected intensities Small excursions to higher x at low resolution are not unusual x is defined as follows X Mean of N 2 1 lt 1 gt N 1 2 0 1 where N equivalents contribute to a given unique reflection reflections with no equivalents are not included in either summation The only optional plots are those that display the distribution of outliers relative to the detector area for each different detector 2theta angle These can show bad pixels or e g a shadow of the beam stop if the active pixel mask was not set correctly in SAINT ice rings and other spatial artifacts but may result in the Postscript file becoming large for large data sets You then have the option of writing the corrected intensities and their standard uncertainties to file in HKLF 4 format fo
14. orrected Data The Postscript plots provide essential diagnostics so we strongly recommend that you create them with a suitable file name for preservation the extension eps will be added if there is no dot in the name You should give them a short title that will appear on each plot The Postscript file is closed before the next question appears so it is a good idea to examine the diagrams with GhostView or GSView before proceeding The first plot gives the variation of scale factors and smoothed Rin as a function of scan and frame number The Rin plot may be subject to relatively wild fluctuations if very few reflections appear per frame The scale factor plot should be almost smooth just showing a little noise see the discussion of the scale factor restraint above The next plot page shows the variation of Rint and Reigma 2 0 l 2 lt l gt as a function of resolution lt provides an indication of the resolution cutoff to be applied to the data and often shows very clearly the improvement of the data as a result of high redundancy In the plot of IE 1I as a function of resolution the curve should stay close to the 0 968 line for a centrosymmetric structure or the 0 736 line for a non centrosymmetric structure especially for large organic or macromolecular structures Values that are uniformly lower than expected may indicate twinning and values that are uniformly higher than expected may be caused by pseudo tra
15. r further processing by XPREP You could apply an additional absorption correction assuming a spherical crystal with given u r where u is the linear absorption coefficient and r is the radius of the equivalent sphere If wisin mm then r should be in mm The dimensions cancel r should be chosen so that it is biased towards the smallest crystal dimension e g if the crystal is a block with dimensions 0 1x0 2x0 3 mm then 0 07mm would be a good value for r This correction is included because the theta dependent part of the absorption cannot be modeled well by comparing equivalent reflections because these invariably have the same 2 theta values However the correction should not be applied if absorption is absent The main affect of applying it will be to increase the equivalent isotropic displacement parameters in the resulting refinement The data can be corrected for lambda 2 contamination Kirschbaum Martin amp Pinkerton J Appl Cryst 30 1997 514 516 The default correction factor of 0 0015 is typical for a sealed tube MoKa SMART system but should be set to zero for a MWPC with CuKa because this detector can successfully discriminate against A 2 radiation in contrast to a CCD or image plate The correction should also be set to zero if mirrors are used instead of a monochromator Since the correction factor is essentially constant for a given system provided that the mA and kV settings of the generator are not cha
16. t in it You should name these files so that the character immediately preceding the dot is 1 2 3 for the different files so that SADABS can generate correct default names for the second and subsequent files If a merged reflection file m raw from SAINT is input to SADABS no further raw files will be requested the two types of files should not be mixed because it could lead to confusion with the scan numbers Although SADABS can read a merged and scaled t raw file from SAINT this is NOT recommended the scaling and filtering algorithms in SADABS are much more sophisticated than in SAINT and deleting reflections prematurely messes up the statistics These files can be large and may take a little time to read in overa network The current version of SADABS for UNIX LINUX systems can handle two million reflections The Windows version is dynamically dimensioned so it asks you for the maximum number of reflections on starting the program If a scan has been processed with the instrument error factor in SAINT not set to the recommended value of zero SADABS will detect this and offer to repair the damage Always accept this offer or you may experience problems with the error model After reading in the data the program checks the direction cosines for consistency The mean error should not exceed about 0 005 Small non zero values may be caused by the crystal wobbling during data collection etc M86 E00046 0102 but larg
17. tion is included the right hand side of the expression for is divided by T f where T is the transmission factor calculated from u t for an infinite lamina Sheldrick amp Sheldrick Acta Cryst B26 1970 1334 1338 and f is either fopp incident and diffracted beam on opposite sides of the plate or fsame both beams on the same side The refined values of u t fopp and fsame are printed each cycle They correct for edge effects and warping of the plate etc This formulation should be regarded as tentative It tends to give a value of u t on the low side because some of the thin plate correction is mopped up by S and P this also gives rise to high correlation factors that slow down the convergence when the thin plate correction is used The refinement is performed using the robust resistant least squares technique pioneered by Prince 1982 in his book Mathematical Techniques in Crystallography and Materials Science This refinement involves weighting down outliers determined using the weighting scheme and is much more stable than arbitrarily eliminating some reflections but not others This method eliminates the need to use the Filter option in SAINT before running SADABS In fact excessive use of Filter will mess up the statistics and lead to wrong esds for the intensities You are far better off not to eliminate any reflections in SAINT i e do NOT use Filter After the required number of cycles have been performe
18. tion requests a high resolution threshold for the data used for parameter refinement ENTER causes no resolution threshold to be applied If the resolution threshold was specified too optimistically when running SAINT we advise you to input a realistic limit here e g 0 9 when the data were processed to 0 7A but the outer 0 2 A was mainly noise Again this setting only affects the parameter determination not the final data processing Now the program asks for a value for the parameter g for the weighting scheme w 0 I lt l gt J that is used for parameter refinement Note that g is determined later in the error analysis Part 2 so the default value of 0 02 can be used in a first pass But if the program later determines a very different value you could M86 E00046 0102 repeat this stage using the new value for g SAINT uses a similar expression with g as the instrument error but with the fundamental flaw that g is multiplied by the intensity of an individual reflection not the corrected mean value lt I gt This will tend to weight up the equivalents with the lowest intensities although they are the one most likely to suffer from absorption or other errors A detailed discussion of this subtle statistical pitfall may be found in the HKL2000 manual It suffices to say here that if the instrument error is set to zero in SAINT SADABS can get the statistics right The instrument error factor depends on th
19. ystal SADABS adds the extension abs if the name has no dot in it The program then displays a list of Laue groups The default number 2 is not always correct Then the program asks about the treatment of Friedel opposites to determine the model used for correcting systematic errors This does NOT affect the final reflection list where Friedel and other equivalents are never merged The answer to this question should usually be Y unless you have a high redundancy and know what you are doing The answer N halves the data to parameter ratio for the determination of the absorption and other parameters If you answer N the program allows you to define the point group so that the Friedel opposites can be correctly identified The default answer to this question is always the chiral point group i e the one that is appropriate for proteins oligonucleotides etc Previous versions of SADABS assumed this point group if the Friedel question was answered with N In the case where the real point group was non centrosymmetric but non chiral this could lead to a slight increase in the apparent amount of racemic twinning and more importantly to difficulties in getting an optimal error model i e reflection esds were a little overestimated which could lead to low GooF values in the refinement Now SADABS asks for the names of the raw files and reads in the data The extension raw is assumed if you type in a name with no do
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