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[dcsuser@bl821k2 denzo_scripts]$ cat auto.dat


[DENZO script for ALS BL8.2.1     ]
  
format ccd adsc unsupported-q210 binned [<--- BL8.2.1 remove binned if appropriate]
  
box print 1.8 1.8
spot elliptical 0.35 0.35 0.0
background elliptical 0.45 0.45 0.0
mosaicity 0.5                      [<--- a rough guess ]
overlap spot
x beam 108.95 y beam  105.1      [BL8.2.1 Jun 2004 ]
  
wavelength 1.1                    [<---- make sure this is correct!]
monochromator 0.9
air absorption length 3145          [<---- wavelength depedent, check Int. tbl.]                                    [<---- or type 'airabs' in csh to estimate it.]
  
error density 0.12                  [<---- detector specific value]
error positional 0.04               [<---- OK for ADSC Q4 detector (0.08mm *1/2)]
error systematic 5.0 partiality 0.1
  
film rotation 90.0
  
crossfire y   .004 x  -.004 xy  -.019
cassette rotx    -.07 roty    -.07 rotz     .00
oscillation start 0.0 range 1.0
profile fitting radius 20.0
space group p43212                     [<----  or use 'lattice <latt. name>']
[lattice monoclinic]
longest vector 300
weak level 5
overload value 65535
distance 128.0                      [<---- check]
resolution limits 25. 3.0
  
TITLE 'data - test'
raw data file '/data/bl821/dcsuser/mydata_1_001.img'  [<---- Check this also]
film output file 'mydata_1_001.x'                     [<---- This too]
sector 1
  
peak search file 'peaks.file'
write predictions
fit cell
fit x beam y beam
fit crystal rotx roty rotz
fit distance
go
  
[Try 'fit all', 'go go go ...' first,]
[   ]

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[dcsuser@bl821k2 denzo_scripts]$ cat batch.com


[batch.dat  ALS BL502 -- insert parameters in between "******" ]
  
title                  'mycryst'
  
format       ccd adsc unsupported-q210 binned
  
wavelength            1.000
air absorption length 3145
skew 0.000
monochromator 0.9
  
film rotation 90.0
  
  
space group            P43212          [ you should know this by now ]
mosaicity              0.75            [ important to have a good estimate! ]
weak level              5.0
box print 1.8 1.8
spot elliptical         0.35 0.35 0.0
background elliptical   0.45 0.45 0.0
overlap                 spot
  
profile fitting radius 30.0
error          density 0.12
error          systematic 5.0 partiality 0.1 positional 0.040
  
  
raw data file          '/data/bl821/dcsuser/mydata_1_###.img' [ <== edit this !]
film output file       'mydata_1_###.x'                      [ <== edit this !]
                                             [ intensities, used by SCALEPACK ]
  
[film york output file  'mydata_###.y']      [ output files that can be fed ]
                                             [ into CCP4 for scaling ]
  
oscillation            start 0.0  range 1    [ phi width per image ]
sector                 1 to 90               [ range of images you want to process ]
write predictions
print zones
  
  
[*************************************************************************]
[ **** insert output from "list" statement of auto-indexing run here **** ]
  
  
[**************************************************************************]
  
  
  
  
[ refinement starts here ]
start refinement
[print no shifts no profiles]      [<===  remove square brackets for shorter log]
                                      
[Insert more 'go's for better convergence in case of tough data]
  
resolution limits      30. 3.0
fit                    crystal rotz  x beam y beam
go go go go go go
  
fit                    crystal rotx  roty
go go go go go go
  
FIT CASSETTE ROTX ROTY
GO GO GO GO GO GO GO GO
FIT CELL
GO GO GO GO GO GO GO GO
  
resolution limits      30  2.0
  
FIT CROSSFIRE X Y XY
GO GO GO GO GO GO GO GO
  
fit all
go go go go go go go go
go go go go go go go go
go go go go go go go go
go go go go go go go go
go go go go go go go go
go go go go go go go go
  
  
  
list
  
[ for integration: ]
fix all
  
print profiles 1 1
  
calculate go
  
end of pack
end of job
  
  
eof
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[dcsuser@bl821k2 denzo_scripts]$ cat scale.com

/usr/local/bin/scalepack << eof-scale > scale.log
resolution 20  1.85
number of zones 20
number of iterations 10
estimated error 0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070
                0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070 0.070
error scale factor 2.0
space group P212121
output file goldenbrown.sca
[scale anomalous]
reference batch  1
add partials 1 to 100
             
format denzo_ip
ignore overloads
postrefine 10
fit crystal a* 1 to 100
fit crystal b* 1 to 100
fit crystal c* 1 to 100
[fit crystal beta* 1 to 100  ]
fit batch rotx  1 to 100
fit batch roty  1 to 100
fit batch mosaicity  1 to 100
 
rejection probability 1e-4
write rejection file
@reject
 
 
sector 1 to 100
FILE  'test_1_###.x'
 
 
 
eof-scale