_ |_) | recognition Release T5.1.2 all rights reserved * * * John Zhong Ren Renz Research, Inc. P. O. Box 605, Westmont, IL 60559, U. S. A. Email renz@renzresearch.com Tel (630) 230-0272 Fax (435) 514-2645 |||)) Welcome to CPLi 0.18.20071112 |||\\ Renz Research, Inc. Precognition: Input I: File & keyboard input (e.g., image & parameters) Quit Q: Exit Precognition (default) Precognition: Script file "limit1.inp" is opened for input. Precognition: Input I: File & keyboard input (e.g., image & parameters) Quit Q: Exit Precognition (default) Precognition: diagnostic off Message of type "diagnostic" is turned off. Precognition: Input I: File & keyboard input (e.g., image & parameters) Quit Q: Exit Precognition (default) Precognition: busy on Message of type "busy" is turned on. Precognition: Input I: File & keyboard input (e.g., image & parameters) Quit Q: Exit Precognition (default) Precognition: Precognition: Input I: File & keyboard input (e.g., image & parameters) Quit Q: Exit Precognition (default) Precognition: Input Precognition:Input: Format F: Image format (f [esrf]) Goniometer G: Goniometer omega, chi, phi (deg; g 0 0 0) Omega O: Omega polar orientation (deg; o -90 0) Crystal X: Crystal info file or cell & SG No Matrix M: Missetting matrix (by row) Distance D: Crystal-detector distance (mm; d 100) Center C: Direct-beam (pxl; c 1000 1000) Center C: Normal projection (c 50 50 normal) Pixel P: Pixel size (mm; p 0.1 0.1) Swing S: Detector swing angles (deg; s 30 0) Tilt T: Detector tilt angle(s) (deg; t 0 [0]) Bulge B: Quadratic & cubic (10^-12; b 0 0) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Format MarCCD Precognition:Input: Format F: Image format (f [esrf]) Goniometer G: Goniometer omega, chi, phi (deg; g 0 0 0) Omega O: Omega polar orientation (deg; o -90 0) Crystal X: Crystal info file or cell & SG No Matrix M: Missetting matrix (by row) Distance D: Crystal-detector distance (mm; d 100) Center C: Direct-beam (pxl; c 1000 1000) Center C: Normal projection (c 50 50 normal) Pixel P: Pixel size (mm; p 0.1 0.1) Swing S: Detector swing angles (deg; s 30 0) Tilt T: Detector tilt angle(s) (deg; t 0 [0]) Bulge B: Quadratic & cubic (10^-12; b 0 0) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Distance 100 ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Crystal-to-detector distance is set to 100 mm. Precognition:Input: Format F: Image format (f [esrf]) Goniometer G: Goniometer omega, chi, phi (deg; g 0 0 0) Omega O: Omega polar orientation (deg; o -90 0) Crystal X: Crystal info file or cell & SG No Matrix M: Missetting matrix (by row) Distance D: Crystal-detector distance (mm; d 100) Center C: Direct-beam (pxl; c 1000 1000) Center C: Normal projection (c 50 50 normal) Pixel P: Pixel size (mm; p 0.1 0.1) Swing S: Detector swing angles (deg; s 30 0) Tilt T: Detector tilt angle(s) (deg; t 0 [0]) Bulge B: Quadratic & cubic (10^-12; b 0 0) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Center 1000.5 1030.5 ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Direct-beam center is set to 1000.5, 1030.5 in pixel. Precognition:Input: Format F: Image format (f [esrf]) Goniometer G: Goniometer omega, chi, phi (deg; g 0 0 0) Omega O: Omega polar orientation (deg; o -90 0) Crystal X: Crystal info file or cell & SG No Matrix M: Missetting matrix (by row) Distance D: Crystal-detector distance (mm; d 100) Center C: Direct-beam (pxl; c 1000 1000) Center C: Normal projection (c 50 50 normal) Pixel P: Pixel size (mm; p 0.1 0.1) Swing S: Detector swing angles (deg; s 30 0) Tilt T: Detector tilt angle(s) (deg; t 0 [0]) Bulge B: Quadratic & cubic (10^-12; b 0 0) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Pixel 0.0792 0.0792 ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Pixel size is set to 0.0792 X 0.0792 in mm. Precognition:Input: Format F: Image format (f [esrf]) Goniometer G: Goniometer omega, chi, phi (deg; g 0 0 0) Omega O: Omega polar orientation (deg; o -90 0) Crystal X: Crystal info file or cell & SG No Matrix M: Missetting matrix (by row) Distance D: Crystal-detector distance (mm; d 100) Center C: Direct-beam (pxl; c 1000 1000) Center C: Normal projection (c 50 50 normal) Pixel P: Pixel size (mm; p 0.1 0.1) Swing S: Detector swing angles (deg; s 30 0) Tilt T: Detector tilt angle(s) (deg; t 0 [0]) Bulge B: Quadratic & cubic (10^-12; b 0 0) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Image images/pyp1_001.mccd ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Image MARCCD165 selected. __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... File images/pyp1_001.mccd is open for read. ............................................................... __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... Loading MAR CCD 165 image file ... Image loaded. ............................................................... File images/pyp1_001.mccd read. __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... Setting sigma image ... \|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\ Done. ............................................................... Precognition:Input: Format F: Image format (f [esrf]) Center C: Normal projection (c 50 50 normal) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Wavelength 1.05 1.4 1.09 Precognition:Input: Format F: Image format (f [esrf]) Center C: Normal projection (c 50 50 normal) Image I: Image or dataset files Spot L: Length, width, sigma & file (pxl; l 8 6 2 [f]) Resolution R: User defaults (A; r 3 20) Wavelength W: User defaults (A; w 0.5 2) Chebyshev V: Maximum degree of spectrum (v 64) Anomalous A: Anomalous scattering (a [on/off]) Quit Q: Exit this menu (default) Precognition:Input: Quit Precognition: Input I: File & keyboard input (e.g., image & parameters) Output O: Save result in files Spot S: Spot recognition (e.g., s file) Dataset D: Process data set Quit Q: Exit Precognition (default) Precognition: Precognition: Input I: File & keyboard input (e.g., image & parameters) Output O: Save result in files Spot S: Spot recognition (e.g., s file) Dataset D: Process data set Quit Q: Exit Precognition (default) Precognition: Spot 10 4 3.7 pyp1_001.spt __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... Finding spots ... |0 found. /0 found. -0 found. \2 found. |4 found. /6 found. -6 found. \8 found. |13 found. /14 found. -18 found. \20 found. |22 found. /25 found. -27 found. \28 found. |31 found. /37 found. -41 found. \43 found. |49 found. /53 found. -58 found. \64 found. |71 found. /80 found. -87 found. \94 found. |102 found. /113 found. -119 found. \129 found. |137 found. /141 found. -149 found. \159 found. |168 found. /177 found. -188 found. \197 found. |208 found. /218 found. -223 found. \230 found. |243 found. /251 found. -260 found. \271 found. |277 found. /287 found. -300 found. \309 found. |321 found. /333 found. -344 found. \349 found. |361 found. /373 found. -384 found. \398 found. |411 found. /417 found. -427 found. \437 found. |448 found. /450 found. -460 found. \478 found. |487 found. /502 found. -511 found. \524 found. |532 found. /546 found. -562 found. \574 found. |588 found. /600 found. -614 found. \625 found. |639 found. /650 found. -663 found. \676 found. |690 found. /696 found. -710 found. \729 found. |739 found. /756 found. -767 found. \780 found. |791 found. /803 found. -812 found. \829 found. |836 found. /845 found. -851 found. \859 found. |878 found. /890 found. -897 found. \912 found. |922 found. /936 found. -945 found. \960 found. |968 found. /979 found. -995 found. \1004 found. |1013 found. /1024 found. -1041 found. \1048 found. |1057 found. /1065 found. -1074 found. \1091 found. |1102 found. /1107 found. -1120 found. \1128 found. |1142 found. /1159 found. -1167 found. \1176 found. |1185 found. /1201 found. -1210 found. \1226 found. |1239 found. /1251 found. -1261 found. \1273 found. |1280 found. /1293 found. -1307 found. \1321 found. |1328 found. /1343 found. -1350 found. \1364 found. |1380 found. /1386 found. -1403 found. \1414 found. |1427 found. /1443 found. -1455 found. \1465 found. |1478 found. /1499 found. -1510 found. \1522 found. |1544 found. /1554 found. -1572 found. \1584 found. |1595 found. /1608 found. -1622 found. \1634 found. |1642 found. /1655 found. -1670 found. \1682 found. |1687 found. /1703 found. -1710 found. \1720 found. |1730 found. /1738 found. -1747 found. \1753 found. |1766 found. /1773 found. -1783 found. \1791 found. |1799 found. /1814 found. -1822 found. \1828 found. |1840 found. /1847 found. -1849 found. \1862 found. |1874 found. /1883 found. -1892 found. \1901 found. |1908 found. /1918 found. -1926 found. \1935 found. |1942 found. /1952 found. -1959 found. \1965 found. |1973 found. /1977 found. -1989 found. \1992 found. |2001 found. /2009 found. -2014 found. \2018 found. |2022 found. /2029 found. -2035 found. \2039 found. |2043 found. /2050 found. -2054 found. \2055 found. |2057 found. /2060 found. -2063 found. \2065 found. |2068 found. /2071 found. -2073 found. \2074 found. |2078 found. /2080 found. -2080 found. \2080 found. | Done. File pyp1_001.spt is overwritten. ............................................................... Precognition: Input I: File & keyboard input (e.g., image & parameters) Output O: Save result in files Spot S: Spot recognition (e.g., s file) Profile F: Spot profile (e.g., f file) Ellipse E: Ellipse recognition Limits L: Soft limits Dataset D: Process data set Quit Q: Exit Precognition (default) Precognition: Profile __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... Finding overall spot profile ... /0% -1% \3% |4% /5% -7% \8% |9% /11% -12% \14% |15% /16% -18% \19% |20% /22% -23% \24% |26% /27% -28% \30% |31% /32% -34% \35% |36% /38% -39% \41% |42% /43% -45% \46% |47% /49% -50% \51% |53% /54% -55% \57% |58% /59% -61% \62% |64% /65% -66% \68% |69% /70% -72% \73% |74% /76% -77% \78% |80% /81% -82% \84% |85% /86% -100% \ Done. ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| 0 0 0 1156.76 950.08 0.0 1.0 0 0 0 959.57 1172.97 0.0 1.0 0 0 0 771.44 802.19 0.0 1.0 0 0 0 955.98 1381.03 0.0 1.0 0 0 0 752.39 837.86 0.0 1.0 0 0 0 1336.85 1044.90 0.0 1.0 0 0 0 870.18 826.23 0.0 1.0 0 0 0 1314.41 865.92 0.0 1.0 0 0 0 1130.27 611.86 0.0 1.0 0 0 0 807.53 794.79 0.0 1.0 0 0 0 765.56 1028.38 0.0 1.0 0 0 0 666.42 746.14 0.0 1.0 0 0 0 1356.11 1366.76 0.0 1.0 0 0 0 1273.35 784.70 0.0 1.0 0 0 0 750.19 1399.72 0.0 1.0 0 0 0 1336.99 1095.85 0.0 1.0 0 0 0 600.22 1178.07 0.0 1.0 0 0 0 708.20 1135.90 0.0 1.0 0 0 0 1124.25 862.76 0.0 1.0 0 0 0 979.34 766.53 0.0 1.0 0 0 0 890.71 687.86 0.0 1.0 0 0 0 1258.68 1338.38 0.0 1.0 0 0 0 652.05 926.62 0.0 1.0 0 0 0 1167.09 847.91 0.0 1.0 0 0 0 1027.52 1333.73 0.0 1.0 0 0 0 1311.44 793.71 0.0 1.0 0 0 0 983.58 662.41 0.0 1.0 0 0 0 1207.30 777.08 0.0 1.0 0 0 0 1149.77 732.47 0.0 1.0 0 0 0 1342.79 882.47 0.0 1.0 0 0 0 1359.57 1223.97 0.0 1.0 0 0 0 646.70 1159.89 0.0 1.0 32 sample spots are used to find an average profile. ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| An overall mean profile is recognized. Semi-major & -minor axes (pixel): 2.58865 1.05309 Non-elliptical correction: 0.000305247 0.0112322 -0.00527107 0.0050105 Non-Gaussian correction: 0.914063 0.780225 Overall spot length is set to 10 pixels. Overall spot width is set to 4 pixels. Estimated crystal dimension is 0.192782 mm. Estimated mosaic spread in FWHM is 0.110279 degree. ............................................................... Precognition: Input I: File & keyboard input (e.g., image & parameters) Output O: Save result in files Spot S: Spot recognition (e.g., s file) Profile F: Spot profile (e.g., f file) Ellipse E: Ellipse recognition Limits L: Soft limits Dataset D: Process data set Quit Q: Exit Precognition (default) Precognition: Limits ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Best sigma cut estimated at 4.45. 1803 real spots on this image. Sigma cut results in 10% noise is 3.87. Suggested sigma cut for indexing and geometry refinement is between 4.45 and 5.84. ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Maximum spot density 9.6/mrad at Bragg angle of 14.3 degree. Diffraction limit estimated at Bragg angle of 21.8 degree or 1.68 A resolution. Suggested resolution for indexing and geometry refinement is 2.11 A. __________ \ ____ / \ \ / / \ \/ / \ / \/ Yield! .................................................... Generating reciprocal lattice points of resolution 1.67826 - 1000 A and wavelength 0 - 2 A ... |/100% - Done. ............................................................... ______ | )_ | Report | | ------ | | ------ | | ------ | | ---- | |________| Lambda-curve peaks at 1 A. Precognition: Input I: File & keyboard input (e.g., image & parameters) Output O: Save result in files Spot S: Spot recognition (e.g., s file) Profile F: Spot profile (e.g., f file) Ellipse E: Ellipse recognition Limits L: Soft limits Dataset D: Process data set Quit Q: Exit Precognition (default) Precognition: Quit