Reflection files obtained from processing by XDS are of type XDS_ASCII. Files specified in this format are used by default in other programs of the XDS package (XSCALE and XDSCONV).

The old file types DIRECT, ANOMAL, NORMAL, OLDHKL, UNIQUE have been used by old versions of XDS (before 2000). Reflection files of these types are still acceptable by XSCALE and XDSCONV.

## DIRECT

XDS.HKL (unformatted direct access) ======= DESCRIPTION OF MAIN OUTPUT FILE The corrected reflection intensities are saved on this file in the current directory. This file is an unformatted direct access file of record length 68 bytes for each reflection. The file is sorted with respect to the unique reflection indices. This means: For each reflection with the original indices H,K,L all symmetry equivalent indices are generated including Friedel related ones. Among all these indices we choose the unique reflection indices HA,KA,LA in the following order: HA is the largest H-index, among those with the same HA-value select those with the largest K-index which is KA, and finally the largest L-index which is called LA. The unique indices HA,KA,LA thus found are packed into a 32-bit word KEY=(LA+511)+(KA+511)*1024+(HA+511)*1048576 . The reflections are then sorted in growing values of KEY. Record structure 16bit-WORD # CONTENTS 1 HA (The last record is indicated by HA=10000) 2 KA HA,KA,LA are the unique reflection indices. 3 LA Any two reflections have the same unique indices if and only if they are related by symmetry. (HA,KA,LA are integer*2) 4 H Original reflection indices H,K,L. 5 K H,K,L are integer*2. 6 L 7 S Identifying number of symmetry operator used to go from original to unique indices. (integer*2). A negative sign indicates that a mirror operation has been applied. This information may be useful if a special treatment for anomalous differences is required which goes beyond the method of the XDS-program. 8 IPEAK Percentage of observed reflection intensity. A value less than 100 indicates either a reflection overlap or bad spots in the profile 9 ICORR Percentage of correlation (integer*2) between observed and expected reflection profile. 10,11 FFADD LP-corrected intensity of this reflection obtained by straight summation of counts within spot region ( background subtracted). The intensity is also corrected for radiation damage and absorption. (real*4) 12,13 SDADD Standard deviation of FFADD.(real*4) 14,15 RLP Reciprocal LP-correction factor (real*4) 16 ABSCAY Combined absorption and decay correction factor*1000 (integer*2). In case you want to remove this calculated correction, divide intensities and standard deviations by ABSCAY/1000.0 . 17 IALFA IALFA and IBETA (both integer*2) are polar- 18 IBETA coordinates of the spindle axis in units of a hundreth of a degree. The lab coordinates of the spindle axis are: Ux=sin(BETA)*cos(ALPHA) Uy=sin(BETA)*sin(ALPHA) Uz=cos(BETA) where ALPHA=IALFA/5729.578, BETA =IBETA/5729.578. 19 IFRM Frame number at diffraction of this reflection (integer*2) 20 PHI Calculated spindle position for this reflection at diffraction in units of a hundreth of a degree. (integer*2) 21 IX, Calculated detector x- and y-coordinates for 22 IY this reflection at diffraction in units of a tenth of a pixel times 512.0/NX and 512.0/NY, respectively. NX, NY are the numbers of pixels along the detector X- and Y-axis. IX,IY are integer*2. 23-28 S0 Laboratory coordinates of direct beam wave- vector ( rec. Angstroem). S0 points from the x-ray source towards the crystal. 29-34 S1 Laboratory coordinates of scattered beam wave- vector. Length is 1.0/lambda (rec. Angstroem) S0 and S1 are real*4 arrays of length 3. S1 points from the crystal towards the detector. At diffraction, laboratory coordinates of the reflection H,K,L are: S1(.)-S0(.)## ANOMAL

ANOMAL.HKL (ASCII, formatted sequential) ========== Description of file format ANOMAL as produced by XDS (ANOMAL.HKL) or XSCALE (XSCALE.HKL) for the compact representation of anomalous intensity data. This file-format will be automatically selected by XDS and XSCALE if a positive value for the input parameter DELFRM is specified (XDS.INP) or greater than FRAME separation (XSCALE.INP). All reflections that are related by crystallographi symmetry are averaged and saved in a single record FORMAT(3 I5,8 E12.4) Each record consists of the following items h,k,l,IwP,SDwP,IwM,SDwM,IP,SDP,IM,SDM h,k,l - unique reflection indices. The file is sorted with respect to these indices. h=10000 indicates the last record in file. IwP,SDwP - Mean weighted intensity and its standard deviation of reflections strictly symmetry related to h, k, l IwM,SDwM - Mean weighted intensity and its standard deviation of reflections strictly symmetry related to -h,-k,-l IP,SDP - Mean unweighted intensity and its standard deviation of reflections strictly symmetry related to h, k, l IM,SDM - Mean unweighted intensity and its standard deviation of reflections strictly symmetry related to -h,-k,-l The unweighted intensities are computed from a restricted set of reflections. Only those reflections are included which form a BIJVOET pair recorded on images separated by less than DELFRM (see XDS.INP) images in the data set. DEFINITIONS and COMMENTS A *negative* standard deviation indicates that the intensity has not been measured. A *zero* standard deviation indicates that -h,-k,-l is strictly symmetry related to h, k, l. Mean *weighted* intensity = SUMi{Ii/SDi**2}/SUMi{1/SDi**2} Mean *unweighted* intensity = SUMi{Ii}/SUMi{1} For computation of the mean *unweighted* intensity, reflection #i is included in the summation only if there exists a different reflection #j such that i,j forms a Bijvoet pair and |image_number(#i) - image_number(#j)| < DELFRM## NORMAL, OLDHKL

NORMAL.HKL (ASCII, formatted sequential) ========== Description of file format NORMAL (or OLDHKL) as produced by XDS (NORMAL.HKL) and XSCALE (XSCALE.HKL) for representing unique intensities in the absence of anomalous scattering effects. Symmetry related reflections including Friedel-pairs are averaged and recorded by FORTRAN FORMAT(3 I5,4 E12.4). Each record consists of the following items h,k,l,I,SDI h,k,l - unique reflection indices. h=10000 indicates the last record in file. I,SDI - Mean weighted intensity and its standard deviation of all reflections symmetry related to h, k, l or -h,-k,-l In case SDI is missing on an input file of this type, XSCALE will assume SDI=0.1*I.## UNIQUE

UNIQUE.HKL (formatted sequential) ========== This file format has been replaced by either ANOMAL or NORMAL, but files of this type may still be used as a reference data set. Symmetry related reflections are averaged and written with FORMAT(3I5,4E12.4). Each record consists of HA,KA,LA,I,Sigma(I),DI,Sigma(DI) HA,KA,LA - unique reflection indices. The file is sorted with respect to these indices. HA=10000 indicates the last record in file. I,Sigma(I) - Mean intensity and its standard deviation. DI,Sigma(DI) - Anomalous intensity difference and its standard deviation. Missing data are indicated by Sigma(DI)<0. DEFINITIONS and COMMENTS 1)Sigma(DI)>0 No missing data ----------- Anomalous scattering effects are possible for HA, KA, LA and expected (as indicated by the input parameter DELFRM>0). I = ('Iw+' + 'Iw-')/2 ; Sigma(I) = standard deviation of I DI = 'I+' - 'I-' ; Sigma(DI)= standard deviation of DI 'Iw-' weighted mean of all reflection intensities which are strictly symmetry related to -HA,-KA,-LA; 'Iw+' weighted mean of all reflection intensities which are strictly symmetry related to HA, KA, LA; 'I+' are the unweighted means of reflections included in the 'I-' estimation of Bijvoet pairs as controlled by the input parameter DELFRM>0. NOTE: 'I+' and 'I-' together with their standard deviations can be recovered in good approximation as : 'I+' = I + DI/2 ; 'I-' = I - DI/2; Sigma('I+')=Sigma('I-')=Sigma(DI)/sqrt(2) which is sufficient information for obtaining Bayesian estimates of structure factor amplitudes and their anomalous scattering differences. This is carried out in the scaling routine XSCALE. 2)Sigma(DI)=0 No missing data ----------- Anomalous scattering effects cannot occur for HA, KA, LA or are negligable (as indicated by the input parameter DELFRM<=0). I = weighted mean of all reflection intensities which have the same unique indices HA,KA,LA; Sigma(I) = standard deviation of I DI = 0 because there is no anomalous scattering effect Sigma(DI)= 0 standard deviation of DI is theoretically 0.0 3)Sigma(DI)<0 Some data are missing in this record. ----------- The value of DI indicates which data are missing. a) DI<0: missing data 'Iw+' and DI. I = 'Iw-' ; Sigma(I) = standard deviation of 'Iw-' b) DI>0: missing data 'Iw-' and DI. I = 'Iw+' ; Sigma(I) = standard deviation of 'Iw+' c) DI=0: missing only data DI. Although both 'Iw+' and 'Iw-' exist, this case may happen because of the value of the input parameter DELFRM which controls acceptance of Bijvoet pairs. I =('Iw+' + 'Iw-')/2; Sigma(I) = standard deviation of I

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