Difference: Jeol2100Information (1 vs. 23)

Revision 2301 Apr 2016 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um
Changed:
<
<

K2 information

  • Size of camera : 3710 x 3838 pixels
  • Pixel size: 5 um
  • Post-film mag : 1.35
>
>

Tietz F416 information

  • Size of camera : 4096 x 4096 pixels
  • Pixel size: 15.6 um
  • Post-film mag : 1.34
 

Tietz CCD CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

Changed:
<
<
  • Late July 2008 - visit by Matthias Stumpf
>
>
  • New Shutterbox installed with new camera; should not need to touch it ever
Deleted:
<
<
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work
 

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
  • Please See Revision 20 of this document for previous Tietz CCD table
Film Magnification CCD Magnification Unbinned Pixel Size (A) Relative Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 50 ND 3252     interpolation with midas
LM 80 ND 2049     interpolation with midas
LM 100 ND 1624     interpolation with midas
LM 150 ND 1036   interpolation with midas
LM 200 ND 761   interpolation with midas
LM 250 ND 615     interpolation with midas
LM 300 ND 500   interpolation with midas
LM 400 ND 384   interpolation with midas
LM 500 ND 310 interpolation with midas
LM 600 ND 262 interpolation with midas
LM 800 ND 199   interpolation with midas
LM 1000 ND 158     interpolation with midas
LM 1200 ND 132     interpolation with midas
LM 1500 ND 106     replica grid squares
LM 2000 ND 75.5   replica grid squares
LM 2500 ND 61.1   replica grid squares
LM 3000 ND 51.2     replica grid squares
LM 4000 ND 38.0 replica grid squares
LM 5000 ND 30.8 replica grid squares
LM 6000 ND 25.6   replica grid squares
>
>
  • Please See Revision 20 of this document for previous Tietz F224 CCD table
  • Please see Revision 22 of this document for Gatan K2 table
Set Magnification CCD Magnification Unbinned Pixel Size (A) Relative Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 50 ND 2320     Based on post-film mag
LM 80 ND 1450     Based on post-film mag
LM 100 ND 1160     Based on post-film mag
LM 150 ND 774   Based on post-film mag
LM 200 ND 580   Based on post-film mag
LM 250 ND 464     Based on post-film mag
LM 300 ND 387   Based on post-film mag
LM 400 ND 292   Based on post-film mag
LM 500 ND 232 Based on post-film mag
LM 600 ND 193 Based on post-film mag
LM 800 ND 145   Based on post-film mag
LM 1000 ND 116     Based on post-film mag
LM 1200 ND 132     nd
LM 1500 ND 106     nd
LM 2000 ND 75.5   nd
LM 2500 ND 61.1   nd
LM 3000 ND 51.2     nd
LM 4000 ND 38.0 nd
LM 5000 ND 30.8 nd
Added:
>
>
LM 6000 ND 25.6   nd
 
MAG 1200 NOT USED        
Changed:
<
<
MAG 1500 ND 99.8 -95.1   replica grid squares
2000 ND ND -94.8   replica grid squares
2500 ND ND ND   replica grid squares 7/23/13 alpha 3
3000 ND ND ND   replica grid squares 7/23/13 alpha 3
4000 ND ND ND   replica grid squares 7/23/13 alpha 3
5000 6,657 7.51 +/- 0.04 (SEM; n=6) 0   replica grid squares 3/16/15 alpha 2
6,000 8,005 6.25 1.19   interpolation with midas from 5000 3/16/15 alpha 2
8,000 10,919 4.58 0.15   interpolation with midas from 5000 3/16/15 alpha 2
10,000 13,661 3.66 0.52   interpolation with midas from 5000 3/16/15 alpha 2
12,000 16,549 3.02 -0.05   interpolation with midas from 5000 and 30,000 3/16/15 alpha 2
15,000 21,267 2.35 -0.19   interpolation with midas from 30,000 3/16/15 alpha 2
20,000 28,634 1.75 -0.22   interpolation with midas from 30,000 3/16/15 alpha 2
25,000 33,971 1.47 2.12   interpolation with midas from 30,000 3/16/15 alpha 2
30,000 39,273 1.27 -1.06   gold diffraction 3/16/15 alpha 2
40,000 52,823 0.95 0.86 38566 +/- 65 gold diffraction; film: TMV 3/16/15 alpha 2
50,000 66,209 0.76 -0.36 48195 +/- 69 gold diffraction; film: TMV 3/16/15 alpha 2
60,000 79,693 0.63 -0.05 57398 +/- 160 gold diffraction; film: TMV 3/16/15 alpha 2
80,000 103,027 0.49 0.01 75560 +/- 230 gold diffraction; film: TMV 3/16/15 alpha 2
100,000 130,051 0.38 0.01   gold diffraction 3/16/15 alpha 2
>
>
MAG 1500 ND 77.4 -95.1   based on post-film mag
2000 2678 58.2 -94.8   replica grid squares
2500 3549 44.0 ND   replica grid squares alpha 2
3000 4371 35.7 ND   replica grid squares alpha 2
4000 5721 27.3 ND   replica grid squares alpha 2
5000 6808 22.9 0   replica grid squares alpha 2
6,000 8,057 19.4 1.19   replica 3/31/16 alpha 2
8,000 11,112 14.0 0.15   replica 3/31/16 alpha 2
10,000 13,305 11.7 0.52   replica 3/31/16 alpha 2
12,000 15,678 9.95 -0.05   replica 3/31/16 alpha 2
15,000 20,425 7.64 -0.19   replica 3/31/16 alpha 2
20,000 25,441 6.13 -0.22   replica 3/31/16 alpha 2
25,000 33,323 4.68 2.12   replica 3/31/16 alpha 2
30,000 41,235 3.78 -1.06   replica 3/31/16 alpha 2
40,000 54,213 2.88 2.88 38566 +/- 65 replica; film: TMV alpha 2
50,000 69,088 2.26 2.26 48195 +/- 69 replica; film: TMV alpha 2
60,000 82,982 1.88 1.88 57398 +/- 160 replica; film: TMV alpha 2
80,000 99,273 1.57 0.01 75560 +/- 230 replica; film: TMV alpha 2
100,000 141,838 1.10 0.01   gold diffraction alpha 2
Added:
>
>
120,000 151,506 1.03
150,000 194,543 0.802
200,000 263,450 0.592
250,000 3221,820 0.485
300,000 380,293 0.410
400,000 517,140 0.302
500,000 635,986 0.245
600,000 798,325 0.195
800,000 1,121,993 0.139
1,000,000 1,344,000 0.116
 
  • Overall CCD to film factor=1.35
  • Resolution limit of this microscope is 1.4A
  • gold lattice: spacing of sputtered gold = 2.347 A.

Defocus Offset using iMDS

March 18, 2014

* Images taken at 50,000X
  • Focus set at 200,000X
  • microscope was at 120keV and first series was taken, then conditioned to 200 keV over 4 hours, let sit ~1 hr, realigned and second series taken, solid carbon grid

  • 200kV
  • Slope: 1.16
  • Offset: 12.17 overfocus

* plot of j2100 df offset at 200 keV:
J2100-200keV.jpg

  • 120kV
  • Slope: 1.39
  • Offset: 16.63 nm underfocus

* plot of j2100 df offset at 120 keV:
J2101-120keV.jpg

May 8, 2014

  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png

-- BillRice - 28 Sep 2007

* 20140318_120-200kVdefocustest.xls: defocus test worksheet

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META FILEATTACHMENT attr="" autoattached="1" comment="defocus test worksheet" date="1395176961" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 200 keV" date="1395176158" name="J2100-200keV.jpg" path="J2100-200keV.jpg" size="27942" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset" date="1368070716" name="j2100_df_offset.png" path="j2100_df_offset.png" size="5769" user="Main.BillRice" version="1"

Revision 2217 Mar 2015 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um
Changed:
<
<

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
>
>

K2 information

  • Size of camera : 3710 x 3838 pixels
  • Pixel size: 5 um
  • Post-film mag : 1.35
Deleted:
<
<
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)
 
Changed:
<
<

CCD : Signal to noise ratio in comparison to film

>
>

Tietz CCD CCD : Signal to noise ratio in comparison to film

 * Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A)down 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 1500 2257 106 212   -141.8   replica grid squares
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 50 74 3252 6504   -70.2   interpolation with midas
>
>
  • Please See Revision 20 of this document for previous Tietz CCD table
Film Magnification CCD Magnification Unbinned Pixel Size (A) Relative Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 50 ND 3252     interpolation with midas
LM 80 ND 2049     interpolation with midas
LM 100 ND 1624     interpolation with midas
LM 150 ND 1036   interpolation with midas
LM 200 ND 761   interpolation with midas
LM 250 ND 615     interpolation with midas
LM 300 ND 500   interpolation with midas
LM 400 ND 384   interpolation with midas
LM 500 ND 310 interpolation with midas
LM 600 ND 262 interpolation with midas
LM 800 ND 199   interpolation with midas
LM 1000 ND 158     interpolation with midas
LM 1200 ND 132     interpolation with midas
LM 1500 ND 106     replica grid squares
LM 2000 ND 75.5   replica grid squares
LM 2500 ND 61.1   replica grid squares
LM 3000 ND 51.2     replica grid squares
LM 4000 ND 38.0 replica grid squares
LM 5000 ND 30.8 replica grid squares
Added:
>
>
LM 6000 ND 25.6   replica grid squares
 
MAG 1200 NOT USED        
Changed:
<
<
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 57.7 +/- 0.07 (n=3) 115   -95.5   replica grid squares 7/23/13 alpha 3
3000 4939 48.28 +/- 0.03 (n=3) 96.6   -95.4   replica grid squares 7/23/13 alpha 3
4000 6578 35.85 +/- 0.09 (n=3) 71.7   -99.0   replica grid squares 7/23/13 alpha 3
5000 8163 29.44 +/- 0.05 (n=3) 58.8 59 -94.0   replica grid squares 7/23/13 alpha 3
6000 9828 24.48 +/- 0.05 (n=2) 49 49 -95.2   replica grid squares 7/23/13 alpha 3
8000 13,413 17.94 +/- 0.04 (n=3) 35.8 36 -95.4   replica grid squares 7/23/13 alpha 3
10000 16,585 14.55 +/- 0.003 (n=3) 29 29 -95.9   replica grid squares 7/23/13 alpha 3
12000 20,082 12.0 +/- 0.1 (n=3) 24 24 -95.9   replica grid squares 7/23/13 alpha 3
15000 25,506 9.48 +/- 0.05 (n=3) 19 19 -95.7   replica grid squares 7/23/13 alpha 3
20000 34,485 6.92 +/- 0.06 (n=3) 13.8 14 -95.5   replica grid squares 7/23/13 alpha 3
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
>
>
MAG 1500 ND 99.8 -95.1   replica grid squares
2000 ND ND -94.8   replica grid squares
2500 ND ND ND   replica grid squares 7/23/13 alpha 3
3000 ND ND ND   replica grid squares 7/23/13 alpha 3
4000 ND ND ND   replica grid squares 7/23/13 alpha 3
5000 6,657 7.51 +/- 0.04 (SEM; n=6) 0   replica grid squares 3/16/15 alpha 2
6,000 8,005 6.25 1.19   interpolation with midas from 5000 3/16/15 alpha 2
8,000 10,919 4.58 0.15   interpolation with midas from 5000 3/16/15 alpha 2
10,000 13,661 3.66 0.52   interpolation with midas from 5000 3/16/15 alpha 2
12,000 16,549 3.02 -0.05   interpolation with midas from 5000 and 30,000 3/16/15 alpha 2
15,000 21,267 2.35 -0.19   interpolation with midas from 30,000 3/16/15 alpha 2
20,000 28,634 1.75 -0.22   interpolation with midas from 30,000 3/16/15 alpha 2
25,000 33,971 1.47 2.12   interpolation with midas from 30,000 3/16/15 alpha 2
30,000 39,273 1.27 -1.06   gold diffraction 3/16/15 alpha 2
40,000 52,823 0.95 0.86 38566 +/- 65 gold diffraction; film: TMV 3/16/15 alpha 2
50,000 66,209 0.76 -0.36 48195 +/- 69 gold diffraction; film: TMV 3/16/15 alpha 2
60,000 79,693 0.63 -0.05 57398 +/- 160 gold diffraction; film: TMV 3/16/15 alpha 2
80,000 103,027 0.49 0.01 75560 +/- 230 gold diffraction; film: TMV 3/16/15 alpha 2
100,000 130,051 0.38 0.01   gold diffraction 3/16/15 alpha 2
  • Overall CCD to film factor=1.35
Deleted:
<
<
150000 243,000 0.986 +/- 0.002 1.972 2 ND ND gold lattice (n=6) 7/23/13 alpha3
200000 332,000 0.722 +/- 0.001 1.44 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
250000 406,000 0.586 +/- 0.0003 1.17 1.4 ND ND gold lattice (n=7) 7/23/13 alpha3
300000 481,000 0.502 +/- 0.0003 1.004 1.4 ND ND gold lattice (n=6) 7/23/13 alpha3
400000 638,000 0.376 +/- 0.001 0.752 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
 
  • Resolution limit of this microscope is 1.4A
Changed:
<
<
  • gold lattice: spacing of sputtered gold = 2.35 A.
>
>
  • gold lattice: spacing of sputtered gold = 2.347 A.
Deleted:
<
<

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1
 

Defocus Offset using iMDS

March 18, 2014

* Images taken at 50,000X
  • Focus set at 200,000X
  • microscope was at 120keV and first series was taken, then conditioned to 200 keV over 4 hours, let sit ~1 hr, realigned and second series taken, solid carbon grid

  • 200kV
  • Slope: 1.16
  • Offset: 12.17 overfocus

* plot of j2100 df offset at 200 keV:
J2100-200keV.jpg

  • 120kV
  • Slope: 1.39
  • Offset: 16.63 nm underfocus

* plot of j2100 df offset at 120 keV:
J2101-120keV.jpg

May 8, 2014

  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png

-- BillRice - 28 Sep 2007

* 20140318_120-200kVdefocustest.xls: defocus test worksheet

META FILEATTACHMENT attr="" autoattached="1" comment="magcal_ july 23 2013" date="1374769298" name="2100cal_072313.zip" path="2100cal_072313.zip" size="104545359" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="defocus test worksheet" date="1395176961" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 200 keV" date="1395176158" name="J2100-200keV.jpg" path="J2100-200keV.jpg" size="27942" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset" date="1368070716" name="j2100_df_offset.png" path="j2100_df_offset.png" size="5769" user="Main.BillRice" version="1"
Deleted:
<
<
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"
 

Revision 2118 Mar 2014 - Main.EdEng

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 57.7 +/- 0.07 (n=3) 115   -95.5   replica grid squares 7/23/13 alpha 3
3000 4939 48.28 +/- 0.03 (n=3) 96.6   -95.4   replica grid squares 7/23/13 alpha 3
4000 6578 35.85 +/- 0.09 (n=3) 71.7   -99.0   replica grid squares 7/23/13 alpha 3
5000 8163 29.44 +/- 0.05 (n=3) 58.8 59 -94.0   replica grid squares 7/23/13 alpha 3
6000 9828 24.48 +/- 0.05 (n=2) 49 49 -95.2   replica grid squares 7/23/13 alpha 3
8000 13,413 17.94 +/- 0.04 (n=3) 35.8 36 -95.4   replica grid squares 7/23/13 alpha 3
10000 16,585 14.55 +/- 0.003 (n=3) 29 29 -95.9   replica grid squares 7/23/13 alpha 3
12000 20,082 12.0 +/- 0.1 (n=3) 24 24 -95.9   replica grid squares 7/23/13 alpha 3
15000 25,506 9.48 +/- 0.05 (n=3) 19 19 -95.7   replica grid squares 7/23/13 alpha 3
20000 34,485 6.92 +/- 0.06 (n=3) 13.8 14 -95.5   replica grid squares 7/23/13 alpha 3
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.986 +/- 0.002 1.972 2 ND ND gold lattice (n=6) 7/23/13 alpha3
200000 332,000 0.722 +/- 0.001 1.44 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
250000 406,000 0.586 +/- 0.0003 1.17 1.4 ND ND gold lattice (n=7) 7/23/13 alpha3
300000 481,000 0.502 +/- 0.0003 1.004 1.4 ND ND gold lattice (n=6) 7/23/13 alpha3
400000 638,000 0.376 +/- 0.001 0.752 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A
  • gold lattice: spacing of sputtered gold = 2.35 A.

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1

Defocus Offset using iMDS

Added:
>
>

March 18, 2014

* Images taken at 50,000X
  • Focus set at 200,000X
  • microscope was at 120keV and first series was taken, then conditioned to 200 keV over 4 hours, let sit ~1 hr, realigned and second series taken, solid carbon grid

  • 200kV
  • Slope: 1.16
  • Offset: 12.17 overfocus

* plot of j2100 df offset at 200 keV:
J2100-200keV.jpg

  • 120kV
  • Slope: 1.39
  • Offset: 16.63 nm underfocus

* plot of j2100 df offset at 120 keV:
J2101-120keV.jpg

May 8, 2014

 
  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png

-- BillRice - 28 Sep 2007

Added:
>
>		 * 20140318_120-200kVdefocustest.xls: defocus test worksheet

META FILEATTACHMENT attr="" autoattached="1" comment="magcal_ july 23 2013" date="1374769298" name="2100cal_072313.zip" path="2100cal_072313.zip" size="104545359" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="defocus test worksheet" date="1395176961" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 200 keV" date="1395176158" name="J2100-200keV.jpg" path="J2100-200keV.jpg" size="27942" user="Main.EdEng" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
Changed:
<
<
META FILEATTACHMENT attachment="2100cal_072313.zip" attr="" comment="magcal_ july 23 2013" date="1374769298" name="2100cal_072313.zip" path="2100cal_072313.zip" size="104545359" stream="2100cal_072313.zip" user="Main.BillRice" version="1"
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset" date="1368070716" name="j2100_df_offset.png" path="j2100_df_offset.png" size="5769" user="Main.BillRice" version="1"
 
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 2025 Jul 2013 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 57.7 +/- 0.07 (n=3) 115   -95.5   replica grid squares 7/23/13 alpha 3
3000 4939 48.28 +/- 0.03 (n=3) 96.6   -95.4   replica grid squares 7/23/13 alpha 3
4000 6578 35.85 +/- 0.09 (n=3) 71.7   -99.0   replica grid squares 7/23/13 alpha 3
5000 8163 29.44 +/- 0.05 (n=3) 58.8 59 -94.0   replica grid squares 7/23/13 alpha 3
6000 9828 24.48 +/- 0.05 (n=2) 49 49 -95.2   replica grid squares 7/23/13 alpha 3
8000 13,413 17.94 +/- 0.04 (n=3) 35.8 36 -95.4   replica grid squares 7/23/13 alpha 3
10000 16,585 14.55 +/- 0.003 (n=3) 29 29 -95.9   replica grid squares 7/23/13 alpha 3
12000 20,082 12.0 +/- 0.1 (n=3) 24 24 -95.9   replica grid squares 7/23/13 alpha 3
15000 25,506 9.48 +/- 0.05 (n=3) 19 19 -95.7   replica grid squares 7/23/13 alpha 3
20000 34,485 6.92 +/- 0.06 (n=3) 13.8 14 -95.5   replica grid squares 7/23/13 alpha 3
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.986 +/- 0.002 1.972 2 ND ND gold lattice (n=6) 7/23/13 alpha3
200000 332,000 0.722 +/- 0.001 1.44 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
250000 406,000 0.586 +/- 0.0003 1.17 1.4 ND ND gold lattice (n=7) 7/23/13 alpha3
300000 481,000 0.502 +/- 0.0003 1.004 1.4 ND ND gold lattice (n=6) 7/23/13 alpha3
400000 638,000 0.376 +/- 0.001 0.752 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A
  • gold lattice: spacing of sputtered gold = 2.35 A.

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1

Defocus Offset using iMDS

  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
Added:
>
>
META FILEATTACHMENT attachment="2100cal_072313.zip" attr="" comment="magcal_ july 23 2013" date="1374769298" name="2100cal_072313.zip" path="2100cal_072313.zip" size="104545359" stream="2100cal_072313.zip" user="Main.BillRice" version="1"
 
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1924 Jul 2013 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
>
>
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration Date
 
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
Changed:
<
<
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
>
>
2500 4118 57.7 +/- 0.07 (n=3) 115   -95.5   replica grid squares 7/23/13 alpha 3
3000 4939 48.28 +/- 0.03 (n=3) 96.6   -95.4   replica grid squares 7/23/13 alpha 3
4000 6578 35.85 +/- 0.09 (n=3) 71.7   -99.0   replica grid squares 7/23/13 alpha 3
5000 8163 29.44 +/- 0.05 (n=3) 58.8 59 -94.0   replica grid squares 7/23/13 alpha 3
6000 9828 24.48 +/- 0.05 (n=2) 49 49 -95.2   replica grid squares 7/23/13 alpha 3
8000 13,413 17.94 +/- 0.04 (n=3) 35.8 36 -95.4   replica grid squares 7/23/13 alpha 3
10000 16,585 14.55 +/- 0.003 (n=3) 29 29 -95.9   replica grid squares 7/23/13 alpha 3
12000 20,082 12.0 +/- 0.1 (n=3) 24 24 -95.9   replica grid squares 7/23/13 alpha 3
15000 25,506 9.48 +/- 0.05 (n=3) 19 19 -95.7   replica grid squares 7/23/13 alpha 3
20000 34,485 6.92 +/- 0.06 (n=3) 13.8 14 -95.5   replica grid squares 7/23/13 alpha 3
 
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
Changed:
<
<
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
>
>
150000 243,000 0.986 +/- 0.002 1.972 2 ND ND gold lattice (n=6) 7/23/13 alpha3
200000 332,000 0.722 +/- 0.001 1.44 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
250000 406,000 0.586 +/- 0.0003 1.17 1.4 ND ND gold lattice (n=7) 7/23/13 alpha3
300000 481,000 0.502 +/- 0.0003 1.004 1.4 ND ND gold lattice (n=6) 7/23/13 alpha3
400000 638,000 0.376 +/- 0.001 0.752 1.4 ND ND gold lattice (n=4) 7/23/13 alpha3
 
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A
Changed:
<
<
>
>
  • gold lattice: spacing of sputtered gold = 2.35 A.
 

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1

Defocus Offset using iMDS

  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1808 May 2013 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1
Added:
>
>

Defocus Offset using iMDS

  • Images taken at 50,000X
  • Focus set at 200,000X
  • experiment done may 8, 2013, 200 kV, solid carbon grid
  • Slope: 1.0
  • Offset: 26 nm underfocus
  • plot of j2100 df offset:
    j2100_df_offset.png
 -- BillRice - 28 Sep 2007

Changed:
<
<
META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
>
>
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="plot of j2100 df offset at 120 keV" date="1395176143" name="J2101-120keV.jpg" path="J2101-120keV.jpg" size="24772" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" user="Main.BillRice" version=""
 
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1705 Mar 2012 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

  • 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)

Aperture Sizes

  • Condenser : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A
Added:
>
>

Magnification Calibration at 120 kV: Jeol 2100F

  • Magnifications calibrated using 23 A layer line of negative stained TMV virus, March 5 2012

Film Magnification Unbinned Pixel Size (A)
50000 2.86
60000 2.835
80000 1.80
d130 1
 -- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1610 Dec 2009 - Main.KdDerr

 
META TOPICPARENT name="CryoEM"
Contents

JEOL 2100 Microscope Parameters

wavelengths

Changed:
<
<		 * 200kV: 0.02508 A
>
>
  • 200kV: 0.02508 A
 

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
Changed:
<
<
  • If CM (alpha) is changed, need to realign beam (voltage center, asigmatism, pivot points)
>
>
  • If CM (alpha) is changed, need to realign beam (voltage center, astigmatism, pivot points)
 

Aperture Sizes

Changed:
<
<
  • Condensor : 200 um, 100 um, 40 um, 10 um
>
>
  • Condenser : 200 um, 100 um, 40 um, 10 um
 
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
Changed:
<
<
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
>
>
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
 
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

Changed:
<
<
  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
>
>
  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
 
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1522 Oct 2009 - Main.KdDerr

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

Microscope Parameters

>
>

JEOL 2100 Microscope Parameters

 

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, asigmatism, pivot points)

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1419 Sep 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, asigmatism, pivot points)

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
Changed:
<
<
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
>
>
LM 50 74 3252 6504   -70.2   interpolation with midas
LM 80 117 2049 4098   -66.6   interpolation with midas
LM 100 148 1624 3248   -67.1   interpolation with midas
LM 150 232 1036 2072   -66.7   interpolation with midas
LM 200 315 761 1522   -67.5   interpolation with midas
LM 250 390 615 1230   -68.6   interpolation with midas
LM 300 480 500 1000   -67.1   interpolation with midas
LM 400 625 384 768   -74.1   interpolation with midas
LM 500 773 310 620   -140.8   interpolation with midas
LM 600 916 262 524   -141.3   interpolation with midas
LM 800 1206 199 398   -142.0   interpolation with midas
LM 1000 1518 158 316   -142.3   interpolation with midas
LM 1200 1825 132 264   -142.2   interpolation with midas
LM 1500 2257 106 212   -141.8   replica grid squares
LM 2000 3180 75.5 151   -143.8   replica grid squares
LM 2500 3925 61.1 122.2   -143.3   replica grid squares
LM 3000 4689 51.2 102.4   -143.0   replica grid squares
LM 4000 6312 38.0 76.0   -142.7   replica grid squares
LM 5000 7795 30.8 61.6   -142.0   replica grid squares
LM 6000 9375 25.6 51.2   -142.0   replica grid squares
 
MAG 1200 NOT USED        
Changed:
<
<
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
>
>
MAG 1500 2404 99.8 199   -95.1   replica grid squares
2000 3251 73.8 148   -94.8   replica grid squares
2500 4118 58.3 116.6   -95.5   replica grid squares
3000 4939 48.6 97.2   -95.4   replica grid squares
4000 6578 36.5 73.0   -99.0   replica grid squares
5000 8163 29.4 58.8 59 -94.0   replica grid squares
6000 9828 24.4 48.8 49 -95.2   replica grid squares
8000 13,413 17.9 35.8 36 -95.4   replica grid squares
10000 16,585 14.5 28.9 29 -95.9   replica grid squares
12000 20,082 11.95 23.9 24 -95.9   replica grid squares
15000 25,506 9.41 18.8 19 -95.7   replica grid squares
20000 34,485 6.96 13.9 14 -95.5   interpolation with midas
25000 40,641 5.91 11.8 12 -97.6   interpolation with midas
30000 46,970 5.11 10.2 10 -96.6   interpolation with midas
40000 63,450 3.78 7.56 7.6 -95.8 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 -95.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 -95.4 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 -95.4 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 -95.4   interpolation with midas
120000 180,933 1.33 2.65 2.7 -95.6   interpolation with midas
 
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1321 Aug 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, asigmatism, pivot points)

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png
Added:
>
>

Shutterbox Information

  • Late July 2008 - visit by Matthias Stumpf
  • He found that the shutter box blanker was connected incorrectly -- now fixed
  • He also found that our box must be opposite to the normal box configuration for the blanking to work
 

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1224 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm
Added:
>
>

Alpha settings

  • Alpha changes CM setting
    • alpha 1: D510
    • alpha 2: 9510
    • alpha 3: 7C50
  • April 24 2008: determined that CM setting of 9D41 gives paralllel beam at 50K mag (no change in image size with changing z height)
  • This is closest to alpha 2, therefore use alpha 2 for most normal use
  • At very high mag (400K), use alpha 1 for parallel beam (otherwise see different defocus in different parts of image)
  • Can use Free Lens Control (or manual mode in iMDS) to set CM to optimum value if desired
  • If CM (alpha) is changed, need to realign beam (voltage center, asigmatism, pivot points)
 

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1117 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
Changed:
<
<
250000        
>
>
250000 406,000 0.591 1.18 1.4 ND ND gold lattice
 
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
  • Resolution limit of this microscope is 1.4A

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 1017 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
>
>
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
 
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000        
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
  • Overall CCD to film factor=1.63
Changed:
<
<
  • Set ALLOWTOPICVIEW =
>
>
  • Resolution limit of this microscope is 1.4A
 -- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 917 Apr 2008 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag
LM 50 74 3252 6504   109.8  
LM 80 117 2049 4098   113.4  
LM 100 148 1624 3248   112.9  
LM 150 232 1036 2072   113.3  
LM 200 315 761 1522   112.5  
LM 250 390 615 1230   111.4  
LM 300 480 500 1000   112.9  
LM 400 625 384 768   105.9  
LM 500 773 310 620   39.2  
LM 600 916 262 524   38.7  
LM 800 1206 199 398   38.0  
LM 1000 1518 158 316   37.7  
LM 1200 1825 132 264   37.8  
LM 1500 2257 106 212   38.2  
LM 2000 3180 75.5 151   36.2  
LM 2500 3925 61.1 122.2   36.7  
LM 3000 4689 51.2 102.4   37.0  
LM 4000 6312 38.0 76.0   37.3  
LM 5000 7795 30.8 61.6   38.0  
LM 6000 9375 25.6 51.2   38.0  
>
>
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag Method of calibration
LM 50 74 3252 6504   109.8   interpolation with midas
LM 80 117 2049 4098   113.4   interpolation with midas
LM 100 148 1624 3248   112.9   interpolation with midas
LM 150 232 1036 2072   113.3   interpolation with midas
LM 200 315 761 1522   112.5   interpolation with midas
LM 250 390 615 1230   111.4   interpolation with midas
LM 300 480 500 1000   112.9   interpolation with midas
LM 400 625 384 768   105.9   interpolation with midas
LM 500 773 310 620   39.2   interpolation with midas
LM 600 916 262 524   38.7   interpolation with midas
LM 800 1206 199 398   38.0   interpolation with midas
LM 1000 1518 158 316   37.7   interpolation with midas
LM 1200 1825 132 264   37.8   interpolation with midas
LM 1500 2257 106 212   38.2   replica grid squares
LM 2000 3180 75.5 151   36.2   replica grid squares
LM 2500 3925 61.1 122.2   36.7   replica grid squares
LM 3000 4689 51.2 102.4   37.0   replica grid squares
LM 4000 6312 38.0 76.0   37.3   replica grid squares
LM 5000 7795 30.8 61.6   38.0   replica grid squares
LM 6000 9375 25.6 51.2   38.0   replica grid squares
 
MAG 1200 NOT USED        
Changed:
<
<
MAG 1500 2404 99.8 199   84.9  
2000 3251 73.8 148   85.2  
2500 4118 58.3 116.6   84.5  
3000 4939 48.6 97.2   84.6  
4000 6578 36.5 73.0   81.0  
5000 8163 29.4 58.8 59 86.0  
6000 9828 24.4 48.8 49 84.8  
8000 13,413 17.9 35.8 36 84.6  
10000 16,585 14.5 28.9 29 84.1  
12000 20,082 11.95 23.9 24 84.1  
15000 25,506 9.41 18.8 19 84.3  
20000 34,485 6.96 13.9 14 84.5  
25000 40,641 5.91 11.8 12 82.4  
30000 46,970 5.11 10.2 10 83.4  
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230
100000 153,952 1.56 3.12 3.1 84.6  
120000 180,933 1.33 2.65 2.7 84.4  
>
>
MAG 1500 2404 99.8 199   84.9   replica grid squares
2000 3251 73.8 148   85.2   replica grid squares
2500 4118 58.3 116.6   84.5   replica grid squares
3000 4939 48.6 97.2   84.6   replica grid squares
4000 6578 36.5 73.0   81.0   replica grid squares
5000 8163 29.4 58.8 59 86.0   replica grid squares
6000 9828 24.4 48.8 49 84.8   replica grid squares
8000 13,413 17.9 35.8 36 84.6   replica grid squares
10000 16,585 14.5 28.9 29 84.1   replica grid squares
12000 20,082 11.95 23.9 24 84.1   replica grid squares
15000 25,506 9.41 18.8 19 84.3   replica grid squares
20000 34,485 6.96 13.9 14 84.5   interpolation with midas
25000 40,641 5.91 11.8 12 82.4   interpolation with midas
30000 46,970 5.11 10.2 10 83.4   interpolation with midas
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65 interpolation with midas; film: TMV
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69 interpolation with midas; film: TMV
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160 interpolation with midas; film: TMV
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230 interpolation with midas; film: TMV
100000 153,952 1.56 3.12 3.1 84.6   interpolation with midas
120000 180,933 1.33 2.65 2.7 84.4   interpolation with midas
Added:
>
>
150000 243,000 0.988 1.976 2 ND ND gold lattice
200000 332,000 0.722 1.44 1.4 ND ND gold lattice
250000        
300000 481,000 0.399 0.798 1.4 ND ND gold lattice
400000 638,000 0.376 0.752 1.4 ND ND gold lattice
500000 819,000 0.293 0.586 1.4 ND ND gold lattice
600000 1.013M 0.237 0.472 1.4 ND ND gold lattice
800000 1.611M 0.149 0.298 1.4 ND ND gold lattice
1000000 2.00M 0.120 0.240 1.4 ND ND gold lattice
 
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 802 Oct 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag
LM 50 74 3252 6504   109.8  
LM 80 117 2049 4098   113.4  
LM 100 148 1624 3248   112.9  
LM 150 232 1036 2072   113.3  
LM 200 315 761 1522   112.5  
LM 250 390 615 1230   111.4  
LM 300 480 500 1000   112.9  
LM 400 625 384 768   105.9  
LM 500 773 310 620   39.2  
LM 600 916 262 524   38.7  
LM 800 1206 199 398   38.0  
LM 1000 1518 158 316   37.7  
LM 1200 1825 132 264   37.8  
LM 1500 2257 106 212   38.2  
LM 2000 3180 75.5 151   36.2  
LM 2500 3925 61.1 122.2   36.7  
LM 3000 4689 51.2 102.4   37.0  
LM 4000 6312 38.0 76.0   37.3  
LM 5000 7795 30.8 61.6   38.0  
LM 6000 9375 25.6 51.2   38.0  
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9  
2000 3251 73.8 148   85.2  
2500 4118 58.3 116.6   84.5  
3000 4939 48.6 97.2   84.6  
4000 6578 36.5 73.0   81.0  
5000 8163 29.4 58.8 59 86.0  
6000 9828 24.4 48.8 49 84.8  
8000 13,413 17.9 35.8 36 84.6  
10000 16,585 14.5 28.9 29 84.1  
12000 20,082 11.95 23.9 24 84.1  
15000 25,506 9.41 18.8 19 84.3  
20000 34,485 6.96 13.9 14 84.5  
25000 40,641 5.91 11.8 12 82.4  
30000 46,970 5.11 10.2 10 83.4  
Changed:
<
<
40000 63,450 3.78 7.56 7.6 84.2  
50000 78,473 3.06 6.12 6.1 84.5  
>
>
40000 63,450 3.78 7.56 7.6 84.2 38566 +/- 65
50000 78,473 3.06 6.12 6.1 84.5 48195 +/- 69
 
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230
100000 153,952 1.56 3.12 3.1 84.6  
120000 180,933 1.33 2.65 2.7 84.4  
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 702 Oct 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag
LM 50 74 3252 6504   109.8  
LM 80 117 2049 4098   113.4  
LM 100 148 1624 3248   112.9  
LM 150 232 1036 2072   113.3  
LM 200 315 761 1522   112.5  
LM 250 390 615 1230   111.4  
LM 300 480 500 1000   112.9  
LM 400 625 384 768   105.9  
LM 500 773 310 620   39.2  
LM 600 916 262 524   38.7  
LM 800 1206 199 398   38.0  
LM 1000 1518 158 316   37.7  
LM 1200 1825 132 264   37.8  
LM 1500 2257 106 212   38.2  
LM 2000 3180 75.5 151   36.2  
LM 2500 3925 61.1 122.2   36.7  
LM 3000 4689 51.2 102.4   37.0  
LM 4000 6312 38.0 76.0   37.3  
LM 5000 7795 30.8 61.6   38.0  
LM 6000 9375 25.6 51.2   38.0  
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9  
2000 3251 73.8 148   85.2  
2500 4118 58.3 116.6   84.5  
3000 4939 48.6 97.2   84.6  
4000 6578 36.5 73.0   81.0  
5000 8163 29.4 58.8 59 86.0  
6000 9828 24.4 48.8 49 84.8  
8000 13,413 17.9 35.8 36 84.6  
10000 16,585 14.5 28.9 29 84.1  
12000 20,082 11.95 23.9 24 84.1  
15000 25,506 9.41 18.8 19 84.3  
20000 34,485 6.96 13.9 14 84.5  
25000 40,641 5.91 11.8 12 82.4  
30000 46,970 5.11 10.2 10 83.4  
40000 63,450 3.78 7.56 7.6 84.2  
50000 78,473 3.06 6.12 6.1 84.5  
Changed:
<
<
60000 94,105 2.55 5.10 5.1 84.6 57430 +/- 300
>
>
60000 94,105 2.55 5.10 5.1 84.6 57398 +/- 160
 
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230
100000 153,952 1.56 3.12 3.1 84.6  
120000 180,933 1.33 2.65 2.7 84.4  
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 601 Oct 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
5000 8163 29.4 58.8 59 86.0
6000 9828 24.4 48.8 49 84.8
8000 13,413 17.9 35.8 36 84.6
10000 16,585 14.5 28.9 29 84.1
12000 20,082 11.95 23.9 24 84.1
15000 25,506 9.41 18.8 19 84.3
20000 34,485 6.96 13.9 14 84.5
25000 40,641 5.91 11.8 12 82.4
30000 46,970 5.11 10.2 10 83.4
40000 63,450 3.78 7.56 7.6 84.2
50000 78,473 3.06 6.12 6.1 84.5
60000 94,105 2.55 5.10 5.1 84.6
80000 123,589 1.94 3.88 3.9 84.6
100000 153,952 1.56 3.12 3.1 84.6
120000 180,933 1.33 2.65 2.7 84.4
>
>
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis Calibrated Film Mag
LM 50 74 3252 6504   109.8  
LM 80 117 2049 4098   113.4  
LM 100 148 1624 3248   112.9  
LM 150 232 1036 2072   113.3  
LM 200 315 761 1522   112.5  
LM 250 390 615 1230   111.4  
LM 300 480 500 1000   112.9  
LM 400 625 384 768   105.9  
LM 500 773 310 620   39.2  
LM 600 916 262 524   38.7  
LM 800 1206 199 398   38.0  
LM 1000 1518 158 316   37.7  
LM 1200 1825 132 264   37.8  
LM 1500 2257 106 212   38.2  
LM 2000 3180 75.5 151   36.2  
LM 2500 3925 61.1 122.2   36.7  
LM 3000 4689 51.2 102.4   37.0  
LM 4000 6312 38.0 76.0   37.3  
LM 5000 7795 30.8 61.6   38.0  
LM 6000 9375 25.6 51.2   38.0  
MAG 1200 NOT USED        
MAG 1500 2404 99.8 199   84.9  
2000 3251 73.8 148   85.2  
2500 4118 58.3 116.6   84.5  
3000 4939 48.6 97.2   84.6  
4000 6578 36.5 73.0   81.0  
5000 8163 29.4 58.8 59 86.0  
6000 9828 24.4 48.8 49 84.8  
8000 13,413 17.9 35.8 36 84.6  
10000 16,585 14.5 28.9 29 84.1  
12000 20,082 11.95 23.9 24 84.1  
15000 25,506 9.41 18.8 19 84.3  
20000 34,485 6.96 13.9 14 84.5  
25000 40,641 5.91 11.8 12 82.4  
30000 46,970 5.11 10.2 10 83.4  
40000 63,450 3.78 7.56 7.6 84.2  
50000 78,473 3.06 6.12 6.1 84.5  
60000 94,105 2.55 5.10 5.1 84.6 57430 +/- 300
80000 123,589 1.94 3.88 3.9 84.6 75560 +/- 230
100000 153,952 1.56 3.12 3.1 84.6  
120000 180,933 1.33 2.65 2.7 84.4  
 
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 528 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

Aperture Sizes

Changed:
<
<
  • 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
>
>
  • Condensor : 200 um, 100 um, 40 um, 10 um
  • Objective : 60 um, 40 um, 30 um, 5 um
  • Selected Area: 120 um, 50 um, 20 um, 10 um
 

CCD information

  • Size of camera : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
5000 8163 29.4 58.8 59 86.0
6000 9828 24.4 48.8 49 84.8
8000 13,413 17.9 35.8 36 84.6
10000 16,585 14.5 28.9 29 84.1
12000 20,082 11.95 23.9 24 84.1
15000 25,506 9.41 18.8 19 84.3
20000 34,485 6.96 13.9 14 84.5
25000 40,641 5.91 11.8 12 82.4
30000 46,970 5.11 10.2 10 83.4
40000 63,450 3.78 7.56 7.6 84.2
50000 78,473 3.06 6.12 6.1 84.5
60000 94,105 2.55 5.10 5.1 84.6
80000 123,589 1.94 3.88 3.9 84.6
100000 153,952 1.56 3.12 3.1 84.6
120000 180,933 1.33 2.65 2.7 84.4
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 428 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

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 : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Changed:
<
<
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (Nyquist) (A) Angle of Tilt Axis
>
>
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) CCD Resolution limit (Nyquist) (A) Angle of Tilt Axis
 
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
Changed:
<
<
5000 8163 29.4 58.8 147 86.0
6000 9828 24.4 48.8 122 84.8
8000 13,413 17.9 35.8 89 84.6
10000 16,585 14.5 28.9 72 84.1
12000 20,082 11.95 23.9 60 84.1
15000 25,506 9.41 18.8 47 84.3
20000 34,485 6.96 13.9 34.8 84.5
25000 40,641 5.91 11.8 29.5 82.4
30000 46,970 5.11 10.2 25.5 83.4
40000 63,450 3.78 7.56 18.9 84.2
50000 78,473 3.06 6.12 15.3 84.5
60000 94,105 2.55 5.10 12.8 84.6
80000 123,589 1.94 3.88 9.7 84.6
100000 153,952 1.56 3.12 7.8 84.6
120000 180,933 1.33 2.65 6.6 84.4
>
>
5000 8163 29.4 58.8 59 86.0
6000 9828 24.4 48.8 49 84.8
8000 13,413 17.9 35.8 36 84.6
10000 16,585 14.5 28.9 29 84.1
12000 20,082 11.95 23.9 24 84.1
15000 25,506 9.41 18.8 19 84.3
20000 34,485 6.96 13.9 14 84.5
25000 40,641 5.91 11.8 12 82.4
30000 46,970 5.11 10.2 10 83.4
40000 63,450 3.78 7.56 7.6 84.2
50000 78,473 3.06 6.12 6.1 84.5
60000 94,105 2.55 5.10 5.1 84.6
80000 123,589 1.94 3.88 3.9 84.6
100000 153,952 1.56 3.12 3.1 84.6
120000 180,933 1.33 2.65 2.7 84.4
 
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 328 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

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 : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)
Added:
>
>

CCD : Signal to noise ratio in comparison to film

* Green: CCD; Red: Film:
backed_vs_ccd.png
 

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (Nyquist) (A) Angle of Tilt Axis
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
5000 8163 29.4 58.8 147 86.0
6000 9828 24.4 48.8 122 84.8
8000 13,413 17.9 35.8 89 84.6
10000 16,585 14.5 28.9 72 84.1
12000 20,082 11.95 23.9 60 84.1
15000 25,506 9.41 18.8 47 84.3
20000 34,485 6.96 13.9 34.8 84.5
25000 40,641 5.91 11.8 29.5 82.4
30000 46,970 5.11 10.2 25.5 83.4
40000 63,450 3.78 7.56 18.9 84.2
50000 78,473 3.06 6.12 15.3 84.5
60000 94,105 2.55 5.10 12.8 84.6
80000 123,589 1.94 3.88 9.7 84.6
100000 153,952 1.56 3.12 7.8 84.6
120000 180,933 1.33 2.65 6.6 84.4
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Changed:
<
<		 * j2100-ccd-film-snr:
>
>
Deleted:
<
<		 backed_vs_ccd.png
 
META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 228 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

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 : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (Nyquist) (A) Angle of Tilt Axis
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
5000 8163 29.4 58.8 147 86.0
6000 9828 24.4 48.8 122 84.8
8000 13,413 17.9 35.8 89 84.6
10000 16,585 14.5 28.9 72 84.1
12000 20,082 11.95 23.9 60 84.1
15000 25,506 9.41 18.8 47 84.3
20000 34,485 6.96 13.9 34.8 84.5
25000 40,641 5.91 11.8 29.5 82.4
30000 46,970 5.11 10.2 25.5 83.4
40000 63,450 3.78 7.56 18.9 84.2
50000 78,473 3.06 6.12 15.3 84.5
60000 94,105 2.55 5.10 12.8 84.6
80000 123,589 1.94 3.88 9.7 84.6
100000 153,952 1.56 3.12 7.8 84.6
120000 180,933 1.33 2.65 6.6 84.4
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

Added:
>
>		 * j2100-ccd-film-snr:
backed_vs_ccd.png

META FILEATTACHMENT attachment="backed_vs_ccd.png" attr="" comment="j2100-ccd-film-snr" date="1190997090" name="backed_vs_ccd.png" path="backed_vs_ccd.png" size="61448" stream="backed_vs_ccd.png" user="Main.BillRice" version="0"
 
META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"

Revision 128 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CryoEM"
Contents

Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f = 2.8 mm
  • Cs = 2.0 mm
  • Chromatic aberration = 2.1 mm

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 : 2048 x 2048 pixels
  • Pixel size: 24 um
  • Post-film mag : 1.63
  • Gain in SerialEM : 44.5 counts / electron (low gain is the setting)
  • Gain in EM Menu3: 178 counts / electron (high gain is the default setting)

Magnification Calibration: Jeol 2100F

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Film Magnification CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Resolution limit (Nyquist) (A) Angle of Tilt Axis
LM 50 74 3252 6504   109.8
LM 80 117 2049 4098   113.4
LM 100 148 1624 3248   112.9
LM 150 232 1036 2072   113.3
LM 200 315 761 1522   112.5
LM 250 390 615 1230   111.4
LM 300 480 500 1000   112.9
LM 400 625 384 768   105.9
LM 500 773 310 620   39.2
LM 600 916 262 524   38.7
LM 800 1206 199 398   38.0
LM 1000 1518 158 316   37.7
LM 1200 1825 132 264   37.8
LM 1500 2257 106 212   38.2
LM 2000 3180 75.5 151   36.2
LM 2500 3925 61.1 122.2   36.7
LM 3000 4689 51.2 102.4   37.0
LM 4000 6312 38.0 76.0   37.3
LM 5000 7795 30.8 61.6   38.0
LM 6000 9375 25.6 51.2   38.0
MAG 1200 NOT USED      
MAG 1500 2404 99.8 199   84.9
2000 3251 73.8 148   85.2
2500 4118 58.3 116.6   84.5
3000 4939 48.6 97.2   84.6
4000 6578 36.5 73.0   81.0
5000 8163 29.4 58.8 147 86.0
6000 9828 24.4 48.8 122 84.8
8000 13,413 17.9 35.8 89 84.6
10000 16,585 14.5 28.9 72 84.1
12000 20,082 11.95 23.9 60 84.1
15000 25,506 9.41 18.8 47 84.3
20000 34,485 6.96 13.9 34.8 84.5
25000 40,641 5.91 11.8 29.5 82.4
30000 46,970 5.11 10.2 25.5 83.4
40000 63,450 3.78 7.56 18.9 84.2
50000 78,473 3.06 6.12 15.3 84.5
60000 94,105 2.55 5.10 12.8 84.6
80000 123,589 1.94 3.88 9.7 84.6
100000 153,952 1.56 3.12 7.8 84.6
120000 180,933 1.33 2.65 6.6 84.4
  • Overall CCD to film factor=1.63
  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

META FILEATTACHMENT attachment="20140318_120-200kVdefocustest.xls" attr="" comment="defocus test worksheet" date="1395176960" name="20140318_120-200kVdefocustest.xls" path="20140318_120-200kVdefocustest.xls" size="20480" stream="20140318_120-200kVdefocustest.xls" user="Main.EdEng" version="1"
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