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aP [1,P1] mP [3,P2] [4,P2(1)]

...ted as CC_{1/2_i}. The difference of the two quantities is ΔCC_1/2. : <math>\Delta CC_{1/2}= CC_{1/2 overall}-CC_{1/2\_i} </math>

character*1 :: axnam(3)=(/'a','b','c'/) open(1,file='XPARM.XDS')

...(ADSC Q315R, SN 930), 2015 : ROTATION_AXIS=1 0 0 whereas in 2010 it was -1 0 0 * BM30A (ESRF, ADSC) has ROTATION_AXIS=-1 0 0 (implemented in [[generate_XDS.INP]] on 2016-10-02)

if(/BEAM +(\S*\d) +(\S*\d)/){ $x=$1; $y=$2; } # get X,Y beam if(/^[^!]*DETECTOR_DISTANCE= *(\S*\d)/) { $d=$1; } # d = detector distance

The program can add a fixed number (default: 1) of adjacent input frames for each output frame. DATA_RANGE= 1 500

1 0 4 48445. 983.361 1 0 5 2124.59 283.825

open(1,file='XDS.INP',status='old') read(1,101,end=98) string

OSCILLATION_RANGE=1 DIRECTION_OF_DETECTOR_X-AXIS=1 0 0

MINIMUM_I/SIGMA=1 WFAC1=1

plot "frames.scales" using 1:3 plot "frames.scales" using 1:9

{| cellpadding="10" cellspacing="0" border="1" | 1 ||-|| 3, 4, 5, 143, 144, 145, 146 || P 1

To analyze XDS_ASCII.HKL in terms of the detailed course of CC_1/2 by frame number and resolution, you could use the program [https:// set multiplot layout 3,1

...329.1 328.9 329.5 120.2 83.7 127.4 1 1 -1 0 1 -1 1 0 -1 -1 -1 0 ...219.6 285.4 329.4 114.5 85.4 109.9 1 1 0 0 -1 0 -1 0 -1 1 1 0

for j in $(seq 1 120); do for j in $(seq 1 100); do

vol=a*b*c*sqrt(1.-cosa**2-cosb**2-cosg**2+2*cosa*cosb*cosg) resol=1./(2.*stol)

To analyze XSCALE.HKL in terms of the detailed course of CC_1/2 by data set number and resolution, you could use the program [https set multiplot layout 3,1

==CC_1/2 calculation== CC_1/2 can be calculated with the so-called σ-τ method ([https://doi.or

...(and re-indexed!) by cell-based assignment as P222₁ and P22₁2, respectively, with ugly consequences for data merging and all downs

INCIDENT_BEAM_DIRECTION=0 0 1 INCLUDE_RESOLUTION_RANGE=50 1

INCLUDE_RESOLUTION_RANGE=50 1 ! optional LABIN FILE 1 ALL

OSCILLATION_RANGE=1.0 !degrees (>0) X-RAY_WAVELENGTH=1.0 !Angstroem

...e:backwardsrotaxis.png|400px|thumb|left|ROTATION_AXIS is -1 0 0 instead of 1 0 0]] [[File:wrongrotaxis.png|400px|thumb|left|ROTATION_AXIS is 0 1 0 instead of 1 0 0]]

NBATCH=1 ...f outlier rejection would be also obtained by using (e.g.) WFAC1=2. NBATCH=1 removes any basic scaling done by CORRECT (as referred to by [https://journ

ntask=$1 #total number of jobs itask=1

:<pre>CBF_DONT_USE_LONG_LONG=1 make all</pre>

* tiny spots (1-2 pixel) 450 frames collected on an ADSC Q315 CCD detector at SSRL BL 11-1. What is special about these data: at the time, it was not clear what the s

''This gives several possible Bravais lattice solutions...e.g. triclinic=1; tetragonal=9. Suppose you want XDS parameters for the tetragonal setting:

usage: xscale_isocluster -dmin <lowres> -dmax <highres> -nbin <nbin> -mode <1 or 2> -dim <dim> -clu <#> -cen <#,#,#,...> -<aAisw> XSCALE_FILE_NAME highres, lowres and nbin (default=1 for low, and 10 for high multiplicity) have the usual meanings.

OSCILLATION_RANGE=1.0 !degrees (>0) X-RAY_WAVELENGTH=1.07176 !Angstroem

...e for XDS-Viewer the pixels go from 0 to NX-1 whereas for XDS they go from 1 to NX).<br />Instead of these files written by XDS, one could directly use # use [[adxv]] for visualization. Otherwise the same as with XDS-Viewer. (1.9.7beta version works for the PILATUS detector at SLS)

# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH 1 -0.0017685 0.0011854-0.0061735 0.0065303 153.13

...if they are found adjacent in 3 dimensions; like x,y,z :: x+1,y,z :: x,y,z+1 :: etc. ...thers will mostly contribute to the integration area (but there is not a 1:1 relationship).

'''1.''' create your XDS.INP file with '''2.''' run for lattice 1:

...rg/pdb/explore.do?structureId=1ZTV JCSG target name TB1631F], resolution 3.1 Å) - evaluated with Qingping Xu; it's one of the [http://www.jcsg.org JCSG ...rcsb.org/pdb/explore.do?structureId=1YCE ATPase C-ring], spacegroup P2₁, resolution 2.4 Å - a large membrane protein structure, 44-fold NCS,

...] (which is a script that XDSGUI uses) assumes that frame numbers start at 1. We then "Save" and "Run XDS". # COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH

...s.html#DIRECTION_OF_DETECTOR_X-AXIS= DIRECTION_OF_DETECTOR_X-AXIS] - often 1 0 0 ...html#DIRECTION_OF_DETECTOR_Y-AXIS= DIRECTION_OF_DETECTOR_Y-AXIS] - often 0 1 0

...is a measure of the non-isomorphism - for isomorphous data, that ratio is 1; for non-isomorphous data, the ratio is lower. This ratio is given in colum ...e program uses a formula (McCoy et al. (2017) PNAS 114, 3637-3641 equation 1) that relates coordinate difference (column 8 of output) to the factor. Thi

<math>\Phi(\mathbf{x} )=\sum_{i=1}^{N-1}\sum_{j=i+1}^{N}\left(cc_{ij}-x_{i}\cdot x_{j}\right)^{2}</math> ...se ratio, long vectors a good signal-to-noise ratio, and vectors of length 1 represent ideal (prototypical) data sets. In fact, the length of each vecto

...to 72 MB in case of the Eiger 16M when running with MAXIMUM_NUBER_OF_JOBS=1. (If DELPHI=20 and OSCILLATION_RANGE=0.05 your computer thus has to have at /usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" || rm "$tempfile"

...t-tasting protein of 207 residues that crystallizes in P4₁2₁2 with a monomer in the asymmetric unit. ...100 K the crystals were soaked for a few seconds in a solution containing 1 M sodium bromide and 25% (v/v) glycerol.

...aset which contains only frames 1-2,46-47,90-91 by specifying a DATA_RANGE=1 91. Although this complained about missing images, it still worked and we u ...they were supposed to exist but do not. --[[User:Mnfodje|Mnfodje]] 15:07, 1 November 2010 (UTC). ''Comment: there is EXCLUDE_DATA_RANGE for this purpos

DATA_RANGE= 1 500 !adjacent input frames for each output frame. (default=1)

...lected with 0.1° oscillation range, at DELPHI=5 and MAXIMUM_NUMBER_OF_JOBS=1) should this be set to 0, to conserve memory and avoid slow processing due ...ecify DATA_RANGE=1 368 (pretending 23 batches of 8°) instead of DATA_RANGE=1 360 . XDS will complain about the missing 8 frames, but that has no adverse

...ed in [[XDSGUI]]'s IDXREF tab (or e.g. with GNUPLOT: plot "SPOT.XDS" using 1:2). TEST_RESOLUTION_RANGE=10. 1.

(1) it looks for possible symmetries of the crystal lattice cell axes could become necessary for space groups P222(1) and P2(1)2(1)2

STARTING_ANGLE= 0.0000 STARTING_FRAME= 1 ROTATION_AXIS= 1.000000 0.000000 0.000000

* shutterless and fast (0.1°/frame, 0.1 sec/frame) With JOB= CORRECT DATA_RANGE= 1 3600,

!1 900 info_array(1) = 1 ! 1=XDS (generic_open may check this)

...he symmetry of the intensity-weighted point lattice (diffraction pattern). 1,2,3,4,6=n-fold rotation axis; -n means inversion centre (normally the - is {| cellpadding="10" cellspacing="0" border="1"

...95.8% 2.9% 3.5% 13978 26.78 3.7% 2.8% 66% 1.623 2115 ...96.5% 4.6% 4.6% 24757 19.46 5.7% 5.5% 46% 1.356 3880

...ust a single one) with int(Z) = n+1, then I consider all aliens with Z > n+1 as outliers. <br /> A different rule of thumb would be to simply consider a ...o judge Wilson outliers is to identify resolution ranges that deviate from 1. in the table '''HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF ACENTRIC DA

# COORDINATES OF REC. BASIS VECTOR LENGTH 1/LENGTH 1 0.0048784-0.0028812 0.0034946 0.0066567 150.22

...e to solve the structure are two runs of 360° collected at a wavelength of 1.9Å. ===dataset 1===

...1 1 SPOT_RANGE=90 90 . Most likely it will be even better with SPOT_RANGE= 1 90 . Also see [[Indexing]]. === reducing WFAC1 below its default of 1 improves my data, right? ===

...ces frame-wise (for XDS_ASCII.HKL) or dataset-wise (for XSCALE.HKL) CC_1/2 statistics is [[XDSCC12]]. ...itially unknown symmetry and cell constants]. This builds upon publication 1. and gives further important details of the IDXREF step, in particular abou

...19828 19942 99.4% 3.5% 4.8% 76973 23.88 4.1% 3.0% -10% 0.599 9080 ...45838 45943 99.8% 8.7% 8.3% 177446 13.94 10.1% 8.4% -2% 0.825 21918

...ndividual reflections (the fine-resolution list in CORRECT.LP) drops below 1 at 3.0 Å resolution. Space group is P212121 with a=91.91 b=92.50 c=119.60 * [[11859_1_E1]], [[11859_1_E2]], [[11859_1_E3]]: at wavelengths of 0.979694, 1.019859, 0.979571 (from the headers) these correspond to inflection, remote

With MAXIMUM_NUMBER_OF_JOBS=1 the plot would definitely not look like this - it would be much smoother be

xds_par 0000000000418951 MAIN__ 1 MAIN_XDS.f90 ***** REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 *****

...and were prepared by James Holton. The files Illuin_microfocus_minimal_00[1-3].tar.bz2 can be [http://bl831.als.lbl.gov/example_data_sets/tarballs down # partial data sets: each of the 100 data sets has only 3 good frames of 1° oscillation; later frames have strong radiation damage

...between shades of gray, and numbers (1000 corresponds to a scalefactor of 1). Along the horizontal axis the frame number (or rather the batch number) i The optimal points for interpolation are near 1/4 and near 3/4 of the total dose. Details are published in [http://dx.doi.o

UNTRUSTED_RECTANGLE=1 3160 3000 3070 TRUSTED_REGION=0 1.5 ! we want the whole detector area

0.000E+00 9.676E+00 1.000E+00 1.000E+00 ../e1_1-372/XDS_ASCII.HKL 0.000E+00 0.000E+00 1.000E+00 1.027E+00 ../e2_1-369/XDS_ASCII.HKL

...ions of XDS since May 10, 2010 print out I/Sigma(I)^asymptotic = 1/&radic;(a*b) as "ISa". ISa is the I/sigma of an infinitely strong reflectio

Visualization of part of the tabular output (tables 1 and 2) may be done with the CCP4 program [http://www.ccp4.ac.uk/html/loggra

...an be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are STANDARD DEVIATION OF SPOT POSITION (PIXELS) 1.80

...a program for generating [[CC1/2|delta-CC_1/2]] and delta-CC_1/2-ano values for XDS_ASCII.HKL (written by [[XDS]]), or for XSCALE.HK usage: xdscc12 [-dmin <lowres>] [-dmax <highres>] [-nbin <nbin>] [-mode <1 or 2>] [-<abcdefstwz>] [-r|-R <ref>] FILE_NAME

...solved with SAD and refined at a resolution of 2.2 A in spacegroup P4(3)2(1)2 (#96). INCLUDE_RESOLUTION_RANGE=40 2.1 ! too weak beyond 2.1 Å

# revision 0.14 . KD 1/2011 - SENSOR_THICKNESS for Pilatus; MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ...n 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction"

...random orientations wrt each other. Each dataset consists of 15 frames of 1 degree rotation. DATA_RANGE= 1 1 ! R-factors involving more than 1 frame are meaningless

...or you (where <code><name-of-library></code> could e.g. be <code>libGLU.so.1</code>). This needs a one-time installation by ...code>apt install hdf5-tools</code>) - but make sure that h5dump is version 1.10 or higher when processing HDF5 data from DLS.

...1%) indicates that the processing has improved; a slight decrease in ISa (<1%) often is accompanied by an increase of CC1/2 at high resolution, and thus ...saved to ~/.xds-gui . The names of the buttons (e.g. "User defined command 1") can be changed by editing ~/.xds-gui .