Difference: TecnaiInformation (1 vs. 26)

Revision 2612 Mar 2015 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 100 um, 50 um, 50 um
    • Have used 70 um aperture, removed 03-06-15, could be put back in
  • Objective : 100 um, 50 um, 50 um, 40 um
    • have 2 spare 100 um apertures 03-06-15
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Tietz F416; installed Jan 2015
  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15.6 um
  • Post-film mag : 1.76 OLD CAMERA
  • Gain: 24 counts / electron

CCD : Signal to noise ratio in comparison to film OLD CAMERA NO LONGER RELEVANT

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
  • Tietz F416 -- done 03-11-2015
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
Changed:
<
<
2100 (LM) 3,624 41.7 83.4 -88  
1,700 2,977 50.7 101.4 74.4  
2,500 4,403 34.4 68.8 90.9  
3,500 6,037 25.0 50.0 91.8  
5,000 8,938 16.8 33.6 91.3  
6,500 11,467 13.0 26.0 91.2  
7,800 13,824 10.8 21.6 91.1  
9,600 17,088 8.80 17.6 91.1  
11,500 20,348 7.55 15.10 91.0  
14,500 25,857 5.91 11.82 90.8  
19,000 33,904 4.46 8.92 91.0  
25,000 42,611 3.56 7.04 90.9  
29,000 50,592 2.99 5.98 90.8  
50,000 88,249 1.71 3.42 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.39 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.07 2.14 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 ND 1.11 ND gold lattice
200,000 357,100 0.420 ND 0.840 ND gold lattice
240,000 427,400 0.351 ND 0.702 ND gold lattice
280,000 505,100 0.297 ND 0.594 ND gold lattice
390,000 694,400 0.216 ND 0.432 ND gold lattice
490,000 862,100 0.174 ND 0.348 ND gold lattice
700,000 1.250M 0.120 ND 0.240 ND gold lattice
>
>
2100 (LM) 3,741 41.7 83.4 -88.59  
1,700 3,077 50.7 101.4 82.99  
2,500 4,535 34.4 68.8 83.31  
3,500 6,240 25.0 50.0 83.69  
5,000 9,286 16.8 33.6 84.03  
6,500 12,000 13.0 26.0 83.95  
7,800 14,444 10.8 21.6 83.89  
9,600 17,727 8.80 17.6 83.9  
11,500 20,662 7.55 15.10 83.92  
14,500 26,396 5.91 11.82 83.91  
19,000 34,978 4.46 8.92 83.90  
25,000 43,820 3.56 7.04 83.87  
29,000 52,174 2.99 5.98 81.69  
50,000 91,228 1.71 3.42 81.67 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 112,230 1.39 2.76 81.59 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 145,794 1.07 2.14 81.52 81,190 +/- 111 (n=4)
100,000 180,765 0.863 1.69 81.4   ND
150,000 268,041 0.582 1.16 81.4 interpolation
200,000 357,798 0.436 0.872 81.37 interpolation
240,000 432,133 0.361 0.722 81.31 interpolation
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
Added:
>
>
700,000 1.250M 0.120 0.240 ND gold lattice
 
Changed:
<
<
  • Average CCD to film factor:
>
>
  • Average CCD to film factor: 1.81
 
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
Deleted:
<
<

Magnification Calibration: Tecnai F20 at 120kV OLD CAAMERA OBSOLETE

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87
 

Defocus Offset for Low dose mode OLD CAMERA

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Defocus Offset for Low dose mode at 120 kV

April 4, 2014 OLD CAMERA
  • line of best fit: df = 1.15* set_df + 1139nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, defocus sets taken: 5 images at 0, then 5 at 500 nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140320-tf20-120kV.jpg

March 27, 2014
  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg

Leginon: Goniometer model OLD CAMERA

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396624753" name="20140320-tf20-120kV.jpg" path="20140320-tf20-120kV.jpg" size="26523" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"

Revision 2511 Mar 2015 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

Changed:
<
<
  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
>
>
  • Condensor : 150 um, 100 um, 50 um, 50 um
    • Have used 70 um aperture, removed 03-06-15, could be put back in
Added:
>
>
  • Objective : 100 um, 50 um, 50 um, 40 um
    • have 2 spare 100 um apertures 03-06-15
 
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

Added:
>
>
  • Tietz F416; installed Jan 2015
 
  • Size of camera : 4096 x 4096 pixels
Changed:
<
<
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron
>
>
  • Pixel size: 15.6 um
  • Post-film mag : 1.76 OLD CAMERA
  • Gain: 24 counts / electron

 
Changed:
<
<

CCD : Signal to noise ratio in comparison to film

>
>

CCD : Signal to noise ratio in comparison to film OLD CAMERA NO LONGER RELEVANT

 
  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Added:
>
>
  • Tietz F416 -- done 03-11-2015
 
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
Changed:
<
<
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice
>
>
2100 (LM) 3,624 41.7 83.4 -88  
1,700 2,977 50.7 101.4 74.4  
2,500 4,403 34.4 68.8 90.9  
3,500 6,037 25.0 50.0 91.8  
5,000 8,938 16.8 33.6 91.3  
6,500 11,467 13.0 26.0 91.2  
7,800 13,824 10.8 21.6 91.1  
9,600 17,088 8.80 17.6 91.1  
11,500 20,348 7.55 15.10 91.0  
14,500 25,857 5.91 11.82 90.8  
19,000 33,904 4.46 8.92 91.0  
25,000 42,611 3.56 7.04 90.9  
29,000 50,592 2.99 5.98 90.8  
50,000 88,249 1.71 3.42 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.39 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.07 2.14 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 ND 1.11 ND gold lattice
200,000 357,100 0.420 ND 0.840 ND gold lattice
240,000 427,400 0.351 ND 0.702 ND gold lattice
280,000 505,100 0.297 ND 0.594 ND gold lattice
390,000 694,400 0.216 ND 0.432 ND gold lattice
490,000 862,100 0.174 ND 0.348 ND gold lattice
700,000 1.250M 0.120 ND 0.240 ND gold lattice
 
Changed:
<
<
  • Average CCD to film factor: 1.76
>
>
  • Average CCD to film factor:
 
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
Changed:
<
<

Magnification Calibration: Tecnai F20 at 120kV

>
>

Magnification Calibration: Tecnai F20 at 120kV OLD CAAMERA OBSOLETE

 
  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87
Changed:
<
<

Defocus Offset for Low dose mode

>
>

Defocus Offset for Low dose mode OLD CAMERA

 
  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Defocus Offset for Low dose mode at 120 kV

Changed:
<
<
April 4, 2014
>
>
April 4, 2014 OLD CAMERA
 
  • line of best fit: df = 1.15* set_df + 1139nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, defocus sets taken: 5 images at 0, then 5 at 500 nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140320-tf20-120kV.jpg

March 27, 2014
  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg
Changed:
<
<

Leginon: Goniometer model

>
>

Leginon: Goniometer model OLD CAMERA

 
  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396624753" name="20140320-tf20-120kV.jpg" path="20140320-tf20-120kV.jpg" size="26523" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"

Revision 2404 Apr 2014 - Main.EdEng

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A

Magnification Calibration: Tecnai F20 at 120kV

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87

Defocus Offset for Low dose mode

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Defocus Offset for Low dose mode at 120 kV

April 4, 2014
Changed:
<
<		 * line of best fit: df = 1.15* set_df + 1139nm
>
>
  • line of best fit: df = 1.15* set_df + 1139nm
 
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, defocus sets taken: 5 images at 0, then 5 at 500 nm, etc...
  • Defocus calculated using ctffind3 software
Added:
>
>
  • plot of tf20 df offset at 120 keV:
  20140320-tf20-120kV.jpg

March 27, 2014
  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396624753" name="20140320-tf20-120kV.jpg" path="20140320-tf20-120kV.jpg" size="26523" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"

Revision 2304 Apr 2014 - Main.EdEng

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A

Magnification Calibration: Tecnai F20 at 120kV

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87

Defocus Offset for Low dose mode

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Defocus Offset for Low dose mode at 120 kV

Added:
>
>
April 4, 2014
* line of best fit: df = 1.15* set_df + 1139nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, defocus sets taken: 5 images at 0, then 5 at 500 nm, etc...
  • Defocus calculated using ctffind3 software 20140320-tf20-120kV.jpg

March 27, 2014
 
  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396624753" name="20140320-tf20-120kV.jpg" path="20140320-tf20-120kV.jpg" size="26523" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"

Revision 2228 Mar 2014 - Main.EdEng

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
Added:
>
>

Magnification Calibration: Tecnai F20 at 120kV

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87
 

Defocus Offset for Low dose mode

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Added:
>
>

Defocus Offset for Low dose mode at 120 kV

  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg
 

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

Added:
>
>
 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"
 

Revision 2102 Dec 2013 - Main.NicolasCoudray

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A

Defocus Offset for Low dose mode

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

Added:
>
>

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

 

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"

Revision 2008 May 2013 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A)down Tilt Axis Angle calibrated film mag
700,000 1.250M 0.120 0.240 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
150,000 270,800 0.554 1.11 ND gold lattice
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
29,000 50,592 2.96 5.93 90.8  
25,000 42,611 3.52 7.04 90.9  
19,000 33,904 4.42 8.85 91.0  
14,500 25,857 5.80 11.60 90.8  
11,500 20,348 7.37 14.74 91.0  
9,600 17,088 8.78 17.56 91.1  
7,800 13,824 10.85 21.7 91.1  
6,500 11,467 13.08 26.2 91.2  
5,000 8,938 16.78 33.6 91.3  
3,500 6,037 24.8 49.7 91.8  
2,500 4,403 34.1 68.1 90.9  
1,700 2,977 50.4 100.8 90.8  
2100 (LM) 3,624 41.4 110 -80.2  

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
Added:
>
>

Defocus Offset for Low dose mode

  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

 

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

Added:
>
>
 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
Changed:
<
<
META FILEATTACHMENT attachment="filmcal_tecnai_2011.zip" attr="" comment="film calibrations 200kv" date="1315428186" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" stream="filmcal_tecnai_2011.zip" user="Main.BillRice" version="1"
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
 

Revision 1907 Sep 2011 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

Added:
>
>		 * filmcal_tecnai_2011.zip: film calibrations 200kv
 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="filmcal.zip" attr="" comment="film calibrations 200kv" date="1315419718" name="filmcal.zip" path="filmcal.zip" size="431408778" stream="filmcal.zip" user="Main.BillRice" version="1"
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
Added:
>
>
META FILEATTACHMENT attachment="filmcal_tecnai_2011.zip" attr="" comment="film calibrations 200kv" date="1315428186" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" stream="filmcal_tecnai_2011.zip" user="Main.BillRice" version="1"
 

Revision 1807 Sep 2011 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
Changed:
<
<
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12)
>
>
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
 
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice

  • Average CCD to film factor: 1.76
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Added:
>
>		 * filmcal.zip: film calibrations 200kv
 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attachment="filmcal.zip" attr="" comment="film calibrations 200kv" date="1315419718" name="filmcal.zip" path="filmcal.zip" size="431408778" stream="filmcal.zip" user="Main.BillRice" version="1"
 

Revision 1707 Sep 2011 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice
>
>
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice
 
  • Average CCD to film factor: 1.76
Added:
>
>
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
 

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 1622 Oct 2009 - Main.KdDerr

 
META TOPICPARENT name="CryoEM"
Changed:
<
<		Contents
>
>

FEI TF20 Microscope Parameters

Deleted:
<
<

Microscope Parameters

 

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice

  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 1512 Feb 2009 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
Changed:
<
<
  • Objective : 70 um, 50 um, 40 um, 20 um
>
>
  • Objective : 50 um, 50 um, 50 um, 40 um
 
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice

  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 1417 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
Changed:
<
<
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice
>
>
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice
 
  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 1317 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
Added:
>
>
150,000 270,800 0.554 1.11 ND ND gold lattice
200,000 357,100 0.420 0.840 ND ND gold lattice
240,000 427,400 0.351 0.702 ND ND gold lattice
280,000 505,100 0.297 0.594 ND ND gold lattice
390,000 694,400 0.216 0.432 ND ND gold lattice
490,000 862,100 0.174 0.348 ND ND gold lattice
700,000 1.250M 0.120 0.240 ND ND gold lattice
 
  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 1204 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4

  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
Added:
>
>		xcal2.png
 
  • Y axis
Added:
>
>		ycal.png
 

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Deleted:
<
<
 
Changed:
<
<		 * leginon x-stage cal:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
Deleted:
<
<		 xcal2.png

* leginon stage y cal:
ycal.png

 
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
Deleted:
<
<
META FILEATTACHMENT attachment="ycal.png" attr="" comment="leginon stage y cal" date="1207331148" name="ycal.png" path="ycal.png" size="10924" stream="ycal.png" user="Main.BillRice" version="0"
 

Revision 1104 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4

  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
  • Y axis

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* leginon x-stage cal:
xcal2.png

Added:
>
>		 * leginon stage y cal:
ycal.png

META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
 
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="xcal2.png" attr="" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" stream="xcal2.png" user="Main.BillRice" version="0"
>
>
META FILEATTACHMENT attachment="ycal.png" attr="" comment="leginon stage y cal" date="1207331148" name="ycal.png" path="ycal.png" size="10924" stream="ycal.png" user="Main.BillRice" version="0"
 

Revision 1004 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4

  • Average CCD to film factor: 1.76

Leginon: Goniometer model

  • X axis
  • Y axis

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Added:
>
>		 * leginon x-stage cal:
xcal2.png
 
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attachment="xcal2.png" attr="" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" stream="xcal2.png" user="Main.BillRice" version="0"
 

Revision 904 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4

  • Average CCD to film factor: 1.76
Added:
>
>

Leginon: Goniometer model

  • X axis
  • Y axis
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 828 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4
>
>
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (3/4 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 110 -80.2
1,700 2,977 50.4 100.8 134 90.8
2,500 4,403 34.1 68.1 91 90.9
3,500 6,037 24.8 49.7 66.3 91.8
5,000 8,938 16.78 33.6 44.8 91.3
6,500 11,467 13.08 26.2 34.9 91.2
7,800 13,824 10.85 21.7 28.9 91.1
9,600 17,088 8.78 17.56 23.4 91.1
11,500 20,348 7.37 14.74 19.6 91.0
14,500 25,857 5.80 11.60 15.5 90.8
19,000 33,904 4.42 8.85 11.8 91.0
25,000 42,611 3.52 7.04 9.4 90.9
29,000 50,592 2.96 5.93 7.9 90.8
50,000 88,249 1.700 3.40 4.5 92.4
62,000 108,857 1.378 2.76 3.7 92.4
80,000 139,813 1.073 2.15 2.9 92.4
 
  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""

Revision 728 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

Changed:
<
<		 * SNR of tecnai CCD:
>
>
  • SNR of tecnai CCD:
  tecnai-ccd.png
Added:
>
>
  • SNR -tecnai film:
    tecnai-film.png
 

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Changed:
<
<		 * snr -tecnai film:
tecnai-film.png
>
>

 
Changed:
<
<
META FILEATTACHMENT attachment="tecnai-ccd.png" attr="" comment="SNR of tecnai CCD" date="1190995416" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" stream="tecnai-ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="tecnai-film.png" attr="" comment="snr -tecnai film" date="1190995548" name="tecnai-film.png" path="tecnai-film.png" size="462385" stream="tecnai-film.png" user="Main.BillRice" version="0"
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
 

Revision 628 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

* SNR of tecnai CCD:
tecnai-ccd.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Added:
>
>		 * snr -tecnai film:
tecnai-film.png
 
META FILEATTACHMENT attachment="tecnai-ccd.png" attr="" comment="SNR of tecnai CCD" date="1190995416" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" stream="tecnai-ccd.png" user="Main.BillRice" version="0"
Added:
>
>
META FILEATTACHMENT attachment="tecnai-film.png" attr="" comment="snr -tecnai film" date="1190995548" name="tecnai-film.png" path="tecnai-film.png" size="462385" stream="tecnai-film.png" user="Main.BillRice" version="0"
 

Revision 528 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

Added:
>
>		 * SNR of tecnai CCD:
tecnai-ccd.png
 
Deleted:
<
<
 

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Changed:
<
<		 * SNR of tecnai CCD:
>
>
Deleted:
<
<		 tecnai-ccd.png
 
META FILEATTACHMENT attachment="tecnai-ccd.png" attr="" comment="SNR of tecnai CCD" date="1190995416" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" stream="tecnai-ccd.png" user="Main.BillRice" version="0"

Revision 428 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

CCD : Signal to noise ratio in comparison to film

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Added:
>
>		 * SNR of tecnai CCD:
tecnai-ccd.png

META FILEATTACHMENT attachment="tecnai-ccd.png" attr="" comment="SNR of tecnai CCD" date="1190995416" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" stream="tecnai-ccd.png" user="Main.BillRice" version="0"
 

Revision 328 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron
Added:
>
>

CCD : Signal to noise ratio in comparison to film

 

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Revision 228 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =
Added:
>
>

Aperture Sizes

  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 70 um, 50 um, 40 um, 20 um
  • Selected Area: 200 um, 100 um, 70 um, 40 um
 

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Revision 128 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

CCD information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (2/5 Nyquist) (A) Tilt Axis Angle
2100 (LM) 3,624 41.4 82.8 207 -80.2
1,700 2,977 50.4 100.8 252 90.8
2,500 4,403 34.1 68.1 170.5 90.9
3,500 6,037 24.8 49.7 124 91.8
5,000 8,938 16.78 33.6 83.9 91.3
6,500 11,467 13.08 26.2 65.4 91.2
7,800 13,824 10.85 21.7 54.3 91.1
9,600 17,088 8.78 17.56 43.9 91.1
11,500 20,348 7.37 14.74 36.9 91.0
14,500 25,857 5.80 11.60 29.0 90.8
19,000 33,904 4.42 8.85 22.1 91.0
25,000 42,611 3.52 7.04 17.6 90.9
29,000 50,592 2.96 5.93 14.8 90.8
50,000 88,249 1.700 3.40 8.5 92.4
62,000 108,857 1.378 2.76 6.9 92.4
80,000 139,813 1.073 2.15 5.4 92.4

  • Average CCD to film factor: 1.76

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

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