Difference: Jeol2100Information (22 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:
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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:
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  • Late July 2008 - visit by Matthias Stumpf
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  • New Shutterbox installed with new camera; should not need to touch it ever
Deleted:
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  • 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:
<
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  • 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:
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LM 6000 ND 25.6   nd
 
MAG 1200 NOT USED        
Changed:
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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
>
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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:
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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

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"
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