Difference between revisions of "Gd-Lysozyme-3-t003.phil"

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Line 3: Line 3:
 
integration {
 
integration {
 
   subpixel_joint_model {
 
   subpixel_joint_model {
  rotations= \
+
rotations= \
   0.09674731   0.07989730   -0.19901338   -0.20726174 \
+
   0.09795939   0.08349210   -0.20361419   -0.20691617 \
  -0.23830834   -0.54561116   -0.32254118   -0.23491938 \
+
  -0.39923060   -0.54209480   -0.43653566   -0.23003526 \
  -0.38213480   -0.40568805   0.00000000  -0.38117534 \
+
  -0.10242422   -0.40710596   0.00000000  -0.55354323 \
  -0.04345543   0.03274763   -0.11864964   -0.09977684 \
+
  -0.00227234   0.00971335   -0.10693288   -0.09601335 \
   0.36115415   0.37260401   0.05477929   0.11149904 \
+
   0.35732751   0.37366355   0.04993701   0.10813432 \
-0.01711986   0.04739852   0.09445341   0.03838210 \
+
  0.09209811   0.08719825   0.07085397   0.04337531 \
   0.32400027   0.13304732   0.00000000   -0.65457856 \
+
   0.27509365   0.10691720   0.00000000   1.26418314 \
   0.08287607   0.07008890   -0.03954289   -0.03622002 \
+
   0.08784942   0.07443324   -0.01190203   -0.04532097 \
  -0.00756307   -0.01077960   -0.08730015   -0.08697513 \
+
  -0.00512166   -0.01107914   -0.08955462   -0.08896718 \
   0.02778883   -0.13734546    0.03048996   0.02011849 \
+
   0.00377937   -0.14850067  -0.15819279   0.01605924 \
-0.07152487   0.29026432   0.00000000    0.06048312 \
+
  0.10442629   0.30097014   0.00000000    0.00000000 \
   0.13779893   0.13067054   -0.16007059   -0.18625599 \
+
   0.14725246   0.12086300   -0.17581044   -0.18857045 \
   0.03336204   0.00450910   0.15636569   0.14043021 \
+
   0.03577268   0.00540184   0.15932964   0.13831522 \
  -0.25321101   -0.29161931   -0.14166711   -0.11677828 \
+
  -0.34188415   -0.30083027   -0.11606445   -0.11739372 \
  0.17978186   0.25283190   0.00000000    0.16777737 \
+
-0.04008142   0.39361071   0.00000000    0.07115385 \
  -0.18476683   -0.20782213   -0.19189638   -0.17657794  \
+
  -0.08882254   -0.22357834   -0.17866009   -0.17357300
  
 
translations= \
 
translations= \
   0.01645599   0.06357114   0.31182856   -0.18587159 \
+
   0.01138666   0.08908748   0.30685503   -0.16366058 \
  -0.33064024  -0.01687369   -0.12924445   0.79448784 \
+
  -0.34040280    0.00489799   -0.13356964   0.82695198 \
  -1.42820923   0.90388123   -0.19540951   0.30820419 \
+
  -1.63444789   1.00840212   -0.18990078   0.35456751 \
  -0.45668958   0.83076082   0.20661251   0.13509025 \
+
  -0.56781276   0.69371881   0.17613032   0.17960829 \
   1.11720423   1.63726722   0.24337533   -0.16778626 \
+
   1.43806650   1.49706731   0.24298697   -0.11418696 \
   0.00000000    0.00000000  -1.58479802   2.73609856 \
+
   0.00000000    0.00000000  -1.61039353   2.71622499 \
   0.61802135   0.93311678   0.28939476   0.02838854 \
+
   0.49659655   0.84873056   0.23416644   0.06339607 \
  -0.49137103   0.40110532   -0.27727766   -0.07446340 \
+
  -0.49159691   0.42130810   -0.28579630   -0.04771136 \
   0.39254526   0.01270432   -0.79533756   -0.06979216 \
+
   0.40396799   0.03458436   -0.78921824   -0.05107363 \
   0.36702082   -0.26706710   0.15538574   -0.14033772 \
+
   0.37149539   -0.24059200   0.18485137   -0.11352443 \
   0.97014944   0.06933318   -0.14560628   0.34449643 \
+
   0.78171995   0.12776378   -0.19006243   0.35734808 \
   0.77364546   -0.63267645   -0.32425343   -0.41274074 \
+
   0.91958122   -0.61123520   -0.35530928   -0.39124163 \
-0.09048855   -0.27351375   0.28195963   0.23814589 \
+
  0.11105022   -0.07804747   0.24755727   0.30765233 \
   0.00000000    0.00000000    2.68328835   -1.12698624 \
+
   0.00000000    0.00000000    0.50147000   -2.98063598 \
   0.46091929   -0.20983287   0.19411799   0.20929951 \
+
   0.45326580   -0.13011659   0.19856685   0.29404793 \
   0.22846055   -0.22224587  -0.01548936   -0.07354274 \
+
   0.25159805   -0.18185393    0.06139230   -0.03307170 \
  -0.07176753   0.12591826   0.36147747   0.16694129 \
+
  -0.06014947   0.15876686   0.36331151   0.19659868 \
  -0.10596766   0.50311655   0.30566388   0.26395658 \
+
  -0.09406686   0.52517409   0.32067849   0.27958553 \
   0.75836529   0.29925123   0.22504273   0.13251012 \
+
   0.81495141   0.23428511   0.27855604   0.12625253 \
   0.33620364   -0.16595709   0.28349104   -0.23108832 \
+
   0.56380094   -0.08960831   0.30332662   -0.19785159 \
   0.49086749   0.91005835   -0.07767814   -0.03281312 \
+
   0.10492892   0.69801869   -0.11844839   -0.10765278 \
   0.00000000    0.00000000    2.05137291   0.20557855 \
+
   0.00000000    0.00000000    0.00000000   0.00000000 \
  0.26748940   0.14474252    0.59710369   -0.22904529 \
+
-0.65023906   0.12419634  -0.30540996   -0.27406762 \
   0.19027123   -0.05061881   -0.40129730   -0.45381425 \
+
   0.22837869   -0.05066519   -0.40744436   -0.44822474 \
  -0.02407400   0.09955869   -0.01526240   -0.03750652 \
+
  -0.01954448   0.11462679   -0.02019565   -0.02985755 \
  -0.17394381   0.23114235   0.34458238   0.09777947 \
+
  -0.17024019   0.24236576   0.34553328   0.11662655 \
   0.33094527   -0.87490899   0.33281045   -0.13360106 \
+
   0.18911301   -0.95155061   0.34060711   -0.11830191 \
   0.04645859   0.07084981   -0.15622817   0.33973182 \
+
   0.03180065   0.06591146   -0.17540330   0.33672156 \
   0.50990247   0.55352531   -0.21437150   0.11181816 \
+
   0.32635750   0.54275894   -0.16189418   0.18520007 \
   0.00000000    0.00000000    0.31198077   3.31932355 \
+
   0.00000000    0.00000000    0.16967828   3.10354466 \
   0.35255043   -0.93410007   0.41454344   -0.24832485 \
+
   0.42318831   -0.84074715   0.43334905   -0.24389003 \
   0.31014590   -0.43458163   0.16026995   0.19435965  \
+
   0.31224335   -0.41763206   0.16475690   0.22534555
  
 
   }
 
   }
 
}
 
}
distl {
+
 
 +
distl{
 
   detector_tiling = None
 
   detector_tiling = None
 
   peripheral_margin = 1
 
   peripheral_margin = 1
Line 75: Line 76:
 
       -1,  0, -1,  0, -1, -1, -1, -1,
 
       -1,  0, -1,  0, -1, -1, -1, -1,
 
       -2,  0, -2,  0,  0,  0,  0,  0,
 
       -2,  0, -2,  0,  0,  0,  0,  0,
       -1,  0, -1,  0, -2, -1, -2, -1,
+
       -2,  0, -2,  0, -2, -1, -2, -1,
  
 
       0, -2,  0, -2,  0, -1,  0, -1,
 
       0, -2,  0, -2,  0, -1,  0, -1,
Line 81: Line 82:
 
       -1, -3, -1, -3,  0,  0,  0,  0,
 
       -1, -3, -1, -3,  0,  0,  0,  0,
 
       -1, -3, -1, -3,  0, -1,  0, -1"""
 
       -1, -3, -1, -3,  0, -1,  0, -1"""
}  
+
}
  
  

Latest revision as of 17:32, 28 September 2014

# -*- mode: conf -*-
integration {
  subpixel_joint_model {
rotations= \
  0.09795939    0.08349210   -0.20361419   -0.20691617  \
 -0.39923060   -0.54209480   -0.43653566   -0.23003526  \
 -0.10242422   -0.40710596    0.00000000   -0.55354323  \
 -0.00227234    0.00971335   -0.10693288   -0.09601335  \
  0.35732751    0.37366355    0.04993701    0.10813432  \
  0.09209811    0.08719825    0.07085397    0.04337531  \
  0.27509365    0.10691720    0.00000000    1.26418314  \
  0.08784942    0.07443324   -0.01190203   -0.04532097  \
 -0.00512166   -0.01107914   -0.08955462   -0.08896718  \
  0.00377937   -0.14850067   -0.15819279    0.01605924  \
  0.10442629    0.30097014    0.00000000    0.00000000  \
  0.14725246    0.12086300   -0.17581044   -0.18857045  \
  0.03577268    0.00540184    0.15932964    0.13831522  \
 -0.34188415   -0.30083027   -0.11606445   -0.11739372  \
 -0.04008142    0.39361071    0.00000000    0.07115385  \
 -0.08882254   -0.22357834   -0.17866009   -0.17357300

translations= \
  0.01138666    0.08908748    0.30685503   -0.16366058  \
 -0.34040280    0.00489799   -0.13356964    0.82695198  \
 -1.63444789    1.00840212   -0.18990078    0.35456751  \
 -0.56781276    0.69371881    0.17613032    0.17960829  \
  1.43806650    1.49706731    0.24298697   -0.11418696  \
  0.00000000    0.00000000   -1.61039353    2.71622499  \
  0.49659655    0.84873056    0.23416644    0.06339607  \
 -0.49159691    0.42130810   -0.28579630   -0.04771136  \
  0.40396799    0.03458436   -0.78921824   -0.05107363  \
  0.37149539   -0.24059200    0.18485137   -0.11352443  \
  0.78171995    0.12776378   -0.19006243    0.35734808  \
  0.91958122   -0.61123520   -0.35530928   -0.39124163  \
  0.11105022   -0.07804747    0.24755727    0.30765233  \
  0.00000000    0.00000000    0.50147000   -2.98063598  \
  0.45326580   -0.13011659    0.19856685    0.29404793  \
  0.25159805   -0.18185393    0.06139230   -0.03307170  \
 -0.06014947    0.15876686    0.36331151    0.19659868  \
 -0.09406686    0.52517409    0.32067849    0.27958553  \
  0.81495141    0.23428511    0.27855604    0.12625253  \
  0.56380094   -0.08960831    0.30332662   -0.19785159  \
  0.10492892    0.69801869   -0.11844839   -0.10765278  \
  0.00000000    0.00000000    0.00000000    0.00000000  \
 -0.65023906    0.12419634   -0.30540996   -0.27406762  \
  0.22837869   -0.05066519   -0.40744436   -0.44822474  \
 -0.01954448    0.11462679   -0.02019565   -0.02985755  \
 -0.17024019    0.24236576    0.34553328    0.11662655  \
  0.18911301   -0.95155061    0.34060711   -0.11830191  \
  0.03180065    0.06591146   -0.17540330    0.33672156  \
  0.32635750    0.54275894   -0.16189418    0.18520007  \
  0.00000000    0.00000000    0.16967828    3.10354466  \
  0.42318831   -0.84074715    0.43334905   -0.24389003  \
  0.31224335   -0.41763206    0.16475690    0.22534555

  }
}

distl{
  detector_tiling = None
  peripheral_margin = 1
  quad_translations =2 -6 4 -6 -6 1 0 -4
  tile_translations = """
       2,  1,  2,  1,  1,  2,  1,  2,
       1,  0,  1,  0,  4,  1,  4,  1,
       2, -2,  2, -2,  0,  0,  0,  0,
       0, -2,  0, -2,  0,  0,  0,  0,

      -1,  0, -1,  0,  0, -1,  0, -1,
      -2,  1, -2,  1, -2,  0, -2,  0,
      -2,  1, -2,  1,  0,  0,  0,  0,
       0,  1,  0,  1, -1,  0, -1,  0,

      -1,  0, -1,  0, -1,  0, -1,  0,
      -1,  0, -1,  0, -1, -1, -1, -1,
      -2,  0, -2,  0,  0,  0,  0,  0,
      -2,  0, -2,  0, -2, -1, -2, -1,

       0, -2,  0, -2,  0, -1,  0, -1,
       0, -4,  0, -4,  0, -4,  0, -4,
      -1, -3, -1, -3,  0,  0,  0,  0,
      -1, -3, -1, -3,  0, -1,  0, -1"""
}





# This is from 4ET8.
target_cell = 79 79 38 90 90 90
known_setting = 9

distl_highres_limit = 1.9
force_method2_resolution_limit = 1.9

mosaicity_limit = 1

# Set to True to pick up second lattice, if present.
#indexing.outlier_detection.switch = True

distl {
  res.outer = 1.9
  minimum_signal_height = 5
  minimum_spot_height = 10
  minimum_spot_area = 1
  spot_area_maximum_factor = 20
  compactness_filter = False
  method2_cutoff_percentage = 5

  # Avoids intensity filter.
  peak_intensity_maximum_factor = 10000
}

indexing {
  # Set to True to generate correction vectors.
  verbose_cv = True
}

integration {
  mask_pixel_value=-2
  background_factor = 2
  detector_gain = 1.0

  #model = use_case_3_simulated_annealing_7
  model = user_supplied

  signal_penetration = 0.5
  #spot_shape_verbose = True
  spotfinder_subset = spots_non-ice
  mosaic {
    refinement_target=ML
    kludge1=1.0 #normally 1.0, but sometimes set to 2.0 to increase indexing
    domain_size_lower_limit=10.
  }

}