Contents
ADSC Quantum 4 Detector Scripts
[NSLS x12b ADSC Quantum Q4 denzo script 3-19-01, px-operations group]
format ccd adsc unsupported-q4
monochromator 0.9
write predictions
print zones
spot elliptical 0.35 0.35 0.0
background elliptical 0.45 0.45 0.0
box print 2.0 2.0
overlap spot
peak search file peaks.file
TITLE 'This title should be between apostrophes'
sector 1
oscillation range 1.000
oscillation start 0.000
raw data file '../apod_1_###.img'
film output file 'apod_1_###.x'
error density 0.70 systematic 5.0 partiality 0.1 positional 0.012
detector rotx 0.0 roty 0.000 rotz 0.000
film rotation 90.000
overload 50000
crossfire y 0.01
crossfire x 0.01
crossfire xy 0.01
X beam 90.34 [These are the same dimensions and origin as the]
Y beam 97.18 [coordinates shown on the right by program hkl -]
[see http://www.px.nsls.bnl.gov/beam_center.cgi]
[for updated coordinates]
distance 250 [Start with the value from CBASS.]
wavelength 0.979 [1 angstrom = 12398.42 eV]
[longest vector 500.] [default is 300, Set if unit cell is big.]
space group p1 [Put in if you know it.]
mosaicity 0.500
resolution limits 30.0 1.8
go [this is the indexing go]
fit all
go [this is the first cycle of refinement go]
sector 1 to 360 [ range of images you want to process ] start refinement print no shifts no profiles resolution limits 2.2 30.0 fit all go go go go go go resolution limits 1.8 30.0 list print profiles 3 3 calculate go end of pack end of job
scalepack << end > scale.log number of iterations 20 number of zones 10 estimated error 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 error scale factor 1.00 rejection probability 0.0001 ignore overloads add partials 1 to 360 resolution 30 2.50 @reject write rejection file 0.8 space group P1 postrefine 10 fit crystal a* 1 to 360 fit crystal b* 1 to 360 fit crystal c* 1 to 360 fit batch rotx 1 to 360 fit batch roty 1 to 360 fit crystal mosxx 1 to 360 format denzo_ip fix b sector 1 to 360 FILE 1 'apod_1_###.x' output file apod.sca end
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Brandeis B4 Detector Scripts
[Version of 2-6-01 PX operations for the Brandeis B4 detector on x12c ]
format ccd unsupported-b4 [Brandeis B4 detector]
monochromator 0.9 [Approx. beam polarization (in hor. plane).]
write predictions
print zones
spot elliptical 0.35 0.35 0.0 [O.K. defaults for 0.2mm collimator.]
background elliptical 0.45 0.45 0.0
box print 2.0 2.0
overlap spot
peak search file peaks.file
TITLE 'This title should be between apostrophes'
sector 1
oscillation range 1.000
oscillation start 0.000
raw data file '../6i3f_###.img'
film output file '6i3f###.x'
error density 1.452 [This is lambda-dependent detector gain.]
detector rotx -0.016 roty 0.000 rotz 0.000
film rotation 90.000
overload 50000
crossfire y 0.01
crossfire x 0.01
crossfire xy 0.01
X beam 99.06 [These are the same dimensions and origin as the]
Y beam 97.12 [coordinates shown on the right by program hkl - ]
[see http://www.px.nsls.bnl.gov/beam_center.cgi]
[for updated coordinates]
distance 150.0
wavelength 1.0000 [1 angstrom = 12398.42 eV]
[longest vector 500.0] [default is 300, Set if unit cell is big.]
space group p1
mosaicity 0.500
resolution limits 30.0 1.8
go [this is the indexing go]
fit all
go [this is the first cycle of refinement go]
sector 1 to 360 [ range of images you want to process ] start refinement print no shifts no profiles resolution limits 2.0 30.0 fit all go go go go go go resolution limits 1.80 30.0 list print profiles 3 3 calculate go end of pack end of job
scalepack << end > scale.log number of iterations 20 number of zones 10 estimated error 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 error scale factor 1.00 rejection probability 0.0001 ignore overloads add partials 1 to 360 resolution 30 1.80 @reject write rejection file 0.8 space group P1 postrefine 10 fit crystal a* 1 to 360 fit crystal b* 1 to 360 fit crystal c* 1 to 360 fit batch rotx 1 to 360 fit batch roty 1 to 360 fit crystal mosxx 1 to 360 format denzo_ip fix b sector 1 to 360 FILE 1 '6i3f###.x' output file 6i3f.sca end
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Brandeis B1.3 Detector Scripts
[Version of 3-26-01 PX operations for the Brandeis B1.3 detector on x12c ]
format ccd brandeis-2k [Brandeis B4 detector]
monochromator 0.9 [Approx. beam polarization (in hor. plane).]
write predictions
print zones
spot elliptical 0.35 0.35 0.0 [O.K. defaults for 0.2mm collimator.]
background elliptical 0.45 0.45 0.0
box print 2.0 2.0
overlap spot
peak search file peaks.file
TITLE 'This title should be between apostrophes'
sector 1
oscillation range 1.000
oscillation start 0.000
raw data file '../6i3f_###.img'
film output file '../6i3f###.x'
error density 1.219 systematic 5.0 partiality 0.1 positional 0.008
[This is lambda-dependent detector gain. Check the chart.]
detector rotx -0.001 roty 0.000 rotz 0.000
film rotation 90.000
overload 50000
crossfire y 0.01
crossfire x 0.01
crossfire xy 0.01
X beam 49.8 [These are the same dimensions and origin as the]
Y beam 54.6 [coordinates shown on the right by program hkl - ]
[see http://www.px.nsls.bnl.gov/beam_center.cgi]
[for updated coordinates]
distance 80.0
wavelength .9202 [1 angstrom = 12398.42 eV]
[longest vector 500.0] [default is 300, Set if unit cell is big.]
space group p1
mosaicity 0.500
resolution limits 30.0 1.8
go [this is the indexing go]
fit all
go [this is the first cycle of refinement go]
sector 1 to 360 [ range of images you want to process ]
start refinement
print no shifts no profiles
resolution limits 2.0 30.0
fit all
go go go go go go
resolution limits 1.80 30.0
list
print profiles 3 3
calculate go
end of pack
end of job
scalepack << end > scale.log
number of iterations 20
number of zones 10
estimated error 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030
error scale factor 1.00
rejection probability 0.0001
ignore overloads
add partials 1 to 360
resolution 30 1.80
@reject
write rejection file 0.8
space group P1
postrefine 10
fit crystal a* 1 to 360
fit crystal b* 1 to 360
fit crystal c* 1 to 360
fit batch rotx 1 to 360
fit batch roty 1 to 360
fit crystal mosxx 1 to 360
format denzo_ip
fix b
sector 1 to 360
FILE 1 '6i3f###.x'
output file 6i3f.sca
end
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ADSC Quantum 315 Detector Scripts
[NSLS x25 ADSC Quantum Q315 denzo script 2-8-02, px-operations group]
format ccd adsc unsupported-q315 binned
monochromator 0.9 [Delete the word "binned" above if]
write predictions [you are running unbinned]
print zones
spot elliptical 0.35 0.35 0.0
background elliptical 0.45 0.45 0.0
box print 2.0 2.0
overlap spot
peak search file peaks.file
TITLE 'This title should be between apostrophes'
sector 1
oscillation range 1.000
oscillation start 0.000
raw data file '../apod_1_###.img'
film output file 'apod_1_###.x'
error density 2.4 systematic 5.0 partiality 0.1 positional 0.025
detector rotx 0.0 roty 0.000 rotz 0.000
film rotation 90.000
overload 65535
crossfire y 0.01
crossfire x 0.01
crossfire xy 0.01
X beam 158.05 [These are the same dimensions and origin as the]
Y beam 151.29 [coordinates shown on the right by program hkl -]
[see http://www.px.nsls.bnl.gov/beam_center.cgi]
[for updated coordinates]
distance 250 [Start with the value from CBASS.]
wavelength 1.1 [1 angstrom = 12398.42 eV]
[longest vector 500.] [default is 300, Set if unit cell is big.]
space group p1 [Put in if you know it.]
mosaicity 0.500
resolution limits 30.0 1.8
go [this is the indexing go]
fit all
go [this is the first cycle of refinement go]
sector 1 to 360 [ range of images you want to process ] start refinement print no shifts no profiles resolution limits 2.2 30.0 fit all go go go go go go resolution limits 1.8 30.0 list print profiles 3 3 calculate go end of pack end of job
scalepack << end > scale.log number of iterations 20 number of zones 10 estimated error 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 0.030 error scale factor 1.00 rejection probability 0.0001 ignore overloads add partials 1 to 360 resolution 30 2.50 @reject write rejection file 0.8 space group P1 postrefine 10 fit crystal a* 1 to 360 fit crystal b* 1 to 360 fit crystal c* 1 to 360 fit batch rotx 1 to 360 fit batch roty 1 to 360 fit crystal mosxx 1 to 360 format denzo_ip fix b sector 1 to 360 FILE 1 'apod_1_###.x' output file apod.sca end
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