powerpoint file available: ~jamesh/powerpoint/ oslo_2010.ppt
TRANSCRIPT
![Page 1: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/1.jpg)
PowerPoint File available:
http://bl831.als.lbl.gov/
~jamesh/powerpoint/
Oslo_2010.ppt
![Page 2: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/2.jpg)
http://ucxray.berkeley.edu/~jamesh/elves
Download Elves from:
![Page 3: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/3.jpg)
Advanced Light Source
![Page 4: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/4.jpg)
Beamline 8.3.1 staff
Acknowledgments
George MeigsGeorge Meigs
Jane Tanamachi
ALS 8.3.1 Team
![Page 5: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/5.jpg)
Acknowledgements
8.3.1 PRT: Jamie CateCenter for Structure of Membrane Proteins
Membrane Protein Expression Center IICenter for HIV Accessory and Regulatory Complexes
W. M. Keck FoundationPlexxikon, Inc.
M D Anderson CRCUniversity of California Berkeley
University of California San FranciscoNational Science Foundation
University of California Campus-Laboratory Collaboration GrantHenry Wheeler
The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences Division, of the US Department of Energy under contract No. DE-AC02-05CH11231 at Lawrence Berkeley National Laboratory.
Ken Frankel Chris Neilson Michael Blum Joe Ferrara
![Page 6: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/6.jpg)
Elves examine images andset-up data processing
Elves run…
mosflmscalasolve
mlpharedm
arp/warp
Elven Automation
![Page 7: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/7.jpg)
Elven Automation
Elves examine images andset-up data processing
Elves run…
mosflmscalasolve
mlpharedm
arp/warp
![Page 8: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/8.jpg)
Elven Automation
Elves examine images andset-up data processing
Elves run…
mosflmscalasolve
mlpharedm
arp/warp
![Page 9: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/9.jpg)
![Page 10: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/10.jpg)
![Page 11: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/11.jpg)
![Page 12: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/12.jpg)
![Page 13: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/13.jpg)
![Page 14: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/14.jpg)
![Page 15: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/15.jpg)
![Page 16: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/16.jpg)
![Page 17: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/17.jpg)
![Page 18: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/18.jpg)
![Page 19: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/19.jpg)
![Page 20: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/20.jpg)
![Page 21: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/21.jpg)
![Page 22: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/22.jpg)
![Page 23: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/23.jpg)
![Page 24: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/24.jpg)
![Page 25: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/25.jpg)
![Page 26: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/26.jpg)
Conversational User Interface
user input ->
![Page 27: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/27.jpg)
Conversational User Interface
user input -> process the data in /data/semet
![Page 28: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/28.jpg)
Conversational User Interface
user input -> process the data in /data/semet
recognition blah blah blah blah /data/semet
![Page 29: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/29.jpg)
Conversational User Interface
user input -> process the data in /data/semet
recognition blah blah blah blah /data/semet
simplify /data/semet
![Page 30: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/30.jpg)
Conversational User Interface
user input -> process the data in /data/semet
recognition blah blah blah blah /data/semet
simplify /data/semet
preempt /data/semet contains image files
![Page 31: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/31.jpg)
Conversational User Interface
user input -> process the data in /data/semet
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 100 mm from the crystal using 1.54 Å x-rays.
![Page 32: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/32.jpg)
Conversational User Interface
user input -> process the data in /data/semet
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 100 mm from the crystal using 1.54 Å x-rays.
confirm Everything look okay? [Yes] ->
![Page 33: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/33.jpg)
Conversational User Interface
user input -> process the data in /data/semet
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 100 mm from the crystal using 1.54 Å x-rays.
confirm Everything look okay? [Yes] ->user input distance was more like 110
![Page 34: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/34.jpg)
Conversational User Interface
user input -> distance was more like 110
![Page 35: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/35.jpg)
Conversational User Interface
user input -> distance was more like 110
recognition distance blah blah blah 110
![Page 36: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/36.jpg)
Conversational User Interface
user input -> distance was more like 110
recognition distance blah blah blah 110
simplify DISTANCE 110
![Page 37: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/37.jpg)
Conversational User Interface
user input -> distance was more like 110
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1.54 Å x-rays.
![Page 38: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/38.jpg)
Conversational User Interface
user input -> distance was more like 110
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1.54 Å x-rays.
confirm Everything look okay? [Yes] ->
![Page 39: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/39.jpg)
Conversational User Interface
user input -> distance was more like 110
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1.54 Å x-rays.
confirm Everything look okay? [Yes]user input -> wavelength is wrong
![Page 40: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/40.jpg)
Conversational User Interface
user input -> wavelength is wrong
![Page 41: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/41.jpg)
Conversational User Interface
user input -> wavelength is wrong
recognition wavelength = -NOT
![Page 42: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/42.jpg)
Conversational User Interface
user input -> wavelength is wrong
recognition wavelength = -NOT
simplify WAVELENGTH
![Page 43: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/43.jpg)
Conversational User Interface
user input -> wavelength is wrong
recognition wavelength = -NOT
query What is the x-ray wavelength? [1.54Å] ->
simplify WAVELENGTH
![Page 44: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/44.jpg)
Conversational User Interface
user input -> wavelength is wrong
recognition wavelength = -NOT
query What is the x-ray wavelength? [1.54Å]user input -> 1
simplify WAVELENGTH
![Page 45: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/45.jpg)
Conversational User Interface
user input -> wavelength is wrong
query What is the x-ray wavelength? [1.54Å]user input -> 1
![Page 46: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/46.jpg)
Conversational User Interface
user input -> wavelength is wrong
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1 Å x-rays.
query What is the x-ray wavelength? [1.54Å]user input -> 1
![Page 47: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/47.jpg)
Conversational User Interface
user input -> wavelength is wrong
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1 Å x-rays.
query What is the x-ray wavelength? [1.54Å]user input -> 1
confirm Everything look okay? [Yes] ->
![Page 48: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/48.jpg)
Conversational User Interface
user input -> wavelength is wrong
report Elves will process from /data/semet/frame001.img to /data/semet/frame100.img Data were collected from 0º to 100º in 1º steps with an ADSC Q4 detector 110 mm from the crystal using 1 Å x-rays.
query What is the x-ray wavelength? [1.54Å]user input -> 1
confirm Everything look okay? [Yes]user input -> Yes
![Page 49: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/49.jpg)
Major Phasing techniques
• Molecular Replacement
• Multiple Isomorphous Replacement
• Multiwavelength Anomalous Diffraction
• Single-wavelength Anomalous Diffraction
![Page 50: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/50.jpg)
?
Molecular Replacementcorrect structure and intensities
http://www.ysbl.york.ac.uk/~cowtan/fourier/coeff.html
![Page 51: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/51.jpg)
Molecular Replacementuse something similar as a starting model
![Page 52: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/52.jpg)
Model Buildingcurrent model is missing something
![Page 53: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/53.jpg)
Model Buildingphases from model
![Page 54: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/54.jpg)
Model Buildingmissing bits show up in “difference map”
![Page 55: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/55.jpg)
Model Buildingmissing bits show up better in FO + (FO - FC) map
![Page 56: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/56.jpg)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1 2 3 4 5 6 7 8 9 10
data
stru
ctu
re f
acto
r (F
)
spot index (h)
Fitting data
![Page 57: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/57.jpg)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1 2 3 4 5 6 7 8 9 10
data
1 param
stru
ctu
re f
acto
r (F
)
spot index (h)
Fitting data
![Page 58: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/58.jpg)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1 2 3 4 5 6 7 8 9 10
data
1 param
3 params
stru
ctu
re f
acto
r (F
)
spot index (h)
Fitting data
![Page 59: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/59.jpg)
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1 2 3 4 5 6 7 8 9 10
data
1 param
3 params
10 params
stru
ctu
re f
acto
r (F
)
spot index (h)
Fitting data
![Page 60: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/60.jpg)
Major Phasing techniques
• Molecular Replacement
• Multiple Isomorphous Replacement
• Multiwavelength Anomalous Diffraction
• Single-wavelength Anomalous Diffraction
![Page 61: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/61.jpg)
inverse Fourier Transformno phase
![Page 62: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/62.jpg)
inverse Fourier Transformno phase
![Page 63: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/63.jpg)
Major Phasing techniques
• Molecular Replacement
• Multiple Isomorphous Replacement
• Multiwavelength Anomalous Diffraction
• Single-wavelength Anomalous Diffraction
![Page 64: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/64.jpg)
dete
ctor
anomalous scattering
sam
ple
x-ray beam
![Page 65: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/65.jpg)
dete
ctoranomalous scattering
sam
ple
x-ray beam
![Page 66: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/66.jpg)
Independent tasks can be performed simultaneously
Multiprocessing Strategy
![Page 67: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/67.jpg)
Multiprocessing Strategy
![Page 68: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/68.jpg)
Multiprocessing Strategy
![Page 69: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/69.jpg)
Multiprocessing Strategy
![Page 70: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/70.jpg)
Multiprocessing Strategy
![Page 71: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/71.jpg)
Multiprocessing Strategy
![Page 72: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/72.jpg)
Multiprocessing Strategy
![Page 73: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/73.jpg)
Multiprocessing Strategy
![Page 74: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/74.jpg)
Multiprocessing Strategy
![Page 75: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/75.jpg)
Multiprocessing Strategy
![Page 76: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/76.jpg)
Multiprocessing Strategy
![Page 77: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/77.jpg)
Multiprocessing Strategy
![Page 78: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/78.jpg)
Multiprocessing Strategy
![Page 79: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/79.jpg)
SOLVE/P212121/doneSOLVE/P21212/doneSOLVE/P21221/doneSOLVE/P22121/doneSOLVE/P2221/doneSOLVE/P2212/doneSOLVE/P2122/busySOLVE/P222/done
Multiprocessing StrategyMultiprocessing Strategy
![Page 80: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/80.jpg)
epmr/P212121/model1/doneepmr/P212121/model2/doneepmr/P21212/model1/doneepmr/P21212/model2/doneepmr/P21221/model1/doneepmr/P21221/model2/doneepmr/P22121/model1/busyepmr/P22121/model2/doneepmr/P2221/model1/epmr/P2221/model2/epmr/P2212/model1/epmr/P2212/model2/epmr/P2122/model1/epmr/P2122/model2/
Multiprocessing Strategy
![Page 81: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/81.jpg)
wARP/P212121/donewARP/P21212/donewARP/P21221/donewARP/P22121/donewARP/P2221/donewARP/P2212/donewARP/P2122/busywARP/P222/done
Multiprocessing Strategy
![Page 82: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/82.jpg)
space group
FOM Rcryst
P3221
P3121
P321
Multiprocessing Advantage
![Page 83: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/83.jpg)
space group
FOM Rcryst
P3221 0.836 0.323
P3121
P321
Multiprocessing Advantage
![Page 84: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/84.jpg)
space group
FOM Rcryst
P3221 0.836 0.323
P3121 0.865 0.196
P321 0.726 0.347
Multiprocessing Advantage
![Page 85: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/85.jpg)
table1.com
![Page 86: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/86.jpg)
table1.com
![Page 87: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/87.jpg)
Elven Automation
How often does it really work?
![Page 88: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/88.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
![Page 89: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/89.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
148 datasets (15 MAD)
![Page 90: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/90.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
148 datasets (15 MAD)
31 investigators
![Page 91: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/91.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
148 datasets (15 MAD)
31 investigators
56 unique cells
![Page 92: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/92.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
148 datasets (15 MAD)
31 investigators
56 unique cells
5 KDa – 23 MDa asymmetric unit
![Page 93: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/93.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
27,686 images collected
148 datasets (15 MAD)
31 investigators
56 unique cells
5 KDa – 23 MDa asymmetric unit
0.94 – 32 Å resolution (3.2 Å)
![Page 94: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/94.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
![Page 95: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/95.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
![Page 96: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/96.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
![Page 97: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/97.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
![Page 98: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/98.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
![Page 99: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/99.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 100: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/100.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 101: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/101.jpg)
Number Description Percent
446028 Images (~7 TB) 33%
2346 Data sets 47%
449 MAD/SAD (1:2) 19%
104 Published 4.4%
8.3.1 in 2003
How many structures get solved?
![Page 102: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/102.jpg)
Why do structures fail?
![Page 103: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/103.jpg)
Overlaps
Why do structures fail?
![Page 104: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/104.jpg)
Overlaps
Signal to noise
Why do structures fail?
![Page 105: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/105.jpg)
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
![Page 106: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/106.jpg)
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
![Page 107: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/107.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 108: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/108.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 109: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/109.jpg)
unavoidable overlaps
![Page 110: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/110.jpg)
unavoidable overlaps
dete
ctor
![Page 111: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/111.jpg)
unavoidable overlaps
phi
dete
ctor
![Page 112: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/112.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
![Page 113: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/113.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
![Page 114: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/114.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 115: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/115.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 116: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/116.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 117: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/117.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 118: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/118.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 119: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/119.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 120: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/120.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
Ewald sphere
![Page 121: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/121.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
b
c
a
![Page 122: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/122.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
b
c
a
![Page 123: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/123.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
b
c
a
![Page 124: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/124.jpg)
unavoidable overlaps
mosaicity
phi
dete
ctor
c*
b
c
a
![Page 125: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/125.jpg)
avoidable overlaps
mosaicity
phi
dete
ctor
c*
b
ca
![Page 126: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/126.jpg)
avoidable overlaps
mosaicity
phi
dete
ctor
c*
bc
a
![Page 127: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/127.jpg)
avoiding overlaps
![Page 128: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/128.jpg)
avoiding overlaps
![Page 129: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/129.jpg)
avoiding overlaps
![Page 130: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/130.jpg)
avoiding overlaps
c
c
![Page 131: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/131.jpg)
avoiding overlaps
1000 mm
![Page 132: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/132.jpg)
avoiding overlaps
1000 mm
2 mrad
10 seconds
![Page 133: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/133.jpg)
avoiding overlaps
1000 mm
2 mm
2 mrad
10 seconds
![Page 134: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/134.jpg)
avoiding overlaps
1000 mm
1 mm
1 mrad
20 seconds
![Page 135: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/135.jpg)
avoiding overlaps
1000 mm
300 um
0.3 mrad
60 seconds
![Page 136: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/136.jpg)
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
![Page 137: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/137.jpg)
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
![Page 138: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/138.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 139: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/139.jpg)
Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
![Page 140: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/140.jpg)
Radiation Damage
why not just avoid it?
![Page 141: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/141.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 142: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/142.jpg)
B ≈ 4 d2 + 120
20
4
0
60
8
0
100
12
0
aver
age
atom
ic B
fac
tor
1 1.5 2 2.5 3 3.5 4 4.5 5
resolution (Å)
![Page 143: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/143.jpg)
Simulated diffraction imageSimulated diffraction imageMLFSOMMLFSOM
simulatedsimulated realreal
![Page 144: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/144.jpg)
signal vs noise
![Page 145: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/145.jpg)
signal vs noise
![Page 146: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/146.jpg)
signal vs noise
“If you don’t have good data,
then you have no data at all.”
-Sung-Hou Kim
![Page 147: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/147.jpg)
signal vs noiseeasy
hard
impossible
![Page 148: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/148.jpg)
signal vs noiseeasy
hard
impossible
threshold of “solvability”
![Page 149: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/149.jpg)
signal vs noise
“If you don’t have good data,
then you must learn statistics.”
-James Holton
![Page 150: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/150.jpg)
Adding noise
![Page 151: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/151.jpg)
Adding noise
12 + 12 = 1.42
![Page 152: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/152.jpg)
Adding noise
12 + 12 = 1.42
32 + 12 = 3.22
σtotal2 = σ1
2 + σ22
![Page 153: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/153.jpg)
Adding noise
12 + 12 = 1.42
32 + 12 = 3.22
σtotal2 = σ1
2 + σ22
![Page 154: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/154.jpg)
Adding noise
12 + 12 = 1.42
32 + 12 = 3.22
σtotal2 = σ1
2 + σ22
![Page 155: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/155.jpg)
Adding noise
12 + 12 = 1.42
32 + 12 = 3.22
102 + 12 = 10.052
![Page 156: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/156.jpg)
MAD phasing simulation
-0.2
0
0.2
0.4
0.6
0.8
1
0.01 0.1 1 10
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t m
odel
mlphare results
![Page 157: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/157.jpg)
SAD phasing simulation
-0.2
0
0.2
0.4
0.6
0.8
1
0.01 0.1 1 10
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t m
odel
mlphare results
![Page 158: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/158.jpg)
SAD phasing experiment
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.5 1.0 1.5 2.0 2.5 3.0
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o pu
blis
hed
mod
el
![Page 159: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/159.jpg)
MR simulation
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0.001 0.01 0.1 1 10 100 1000
Signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t de
nsity
corrupted data
![Page 160: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/160.jpg)
“photon counting”
Read-out noise
Shutter jitter
Beam flicker
spot shape
radiation damage
σ(N) = sqrt(N)
rms 11.5 e-/pixel
rms 0.57 ms
0.15 %/√Hz
pixels? mosaicity?
B/Gray?
signal vs noise
![Page 161: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/161.jpg)
Which error dominates?
• Weak spots (high-res)background
• MAD/SAD (small differences)detector calibration
( if not rad dam! )
![Page 162: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/162.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 163: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/163.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 164: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/164.jpg)
Background level sets needed photons/spot
Moukhametzianov et al. (2008). Acta Cryst. D 64, 158-166
![Page 165: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/165.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 166: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/166.jpg)
Optimal exposure time(faint spots)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
too long!
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
![Page 167: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/167.jpg)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
Optimal exposure time(faint spots)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
too short!
![Page 168: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/168.jpg)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
Optimal exposure time(faint spots)
σtotal2 = Nphotons
+ σreadout2+ σraddam
2
needlessly long
![Page 169: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/169.jpg)
Nphotons ≈ σdetector2
Optimal exposure time(faint spots)
“optimal”
![Page 170: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/170.jpg)
Nphotons ≈ 10x σdetector2
Optimal exposure time(faint spots)
“buried”
![Page 171: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/171.jpg)
Nspot + Nbg ≈ 10x m
Optimal exposure time(faint spots)
“buried”
2
0
gain
![Page 172: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/172.jpg)
0 + Nbg ≈ 10x m
Optimal exposure time(faint spots)
“buried”
2
0
gain
![Page 173: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/173.jpg)
Optimal exposure time(faint spots)
2
00 10
gain
mgain
bgbghr
![Page 174: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/174.jpg)
Optimal exposure time(faint spots)
2
00 10
gain
mt
t
gain
bgbg
ref
hrref
![Page 175: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/175.jpg)
Optimal exposure time(faint spots)
0
2010
bgbggain
mtt
refrefhr
thr Optimal exposure time for data set (s)tref exposure time of reference image (s)bgref background level near weak spots on
reference image (ADU)bg0 ADC offset of detector (ADU)bghr optimal background level (via thr)σ0 rms read-out noise (ADU)gain ADU/photonm multiplicity of data set (including partials)
Short answer:
bghr ~ 100 ADU
for ADSC Q315r
![Page 176: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/176.jpg)
What error dominates?
• Weak spots (high-res)background
• MAD/SAD (small differences)detector calibration
if not rad dam!
![Page 177: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/177.jpg)
Optimal exposure time(anomalous differences)
I-I+
3%
100
phot
ons
10 photons
100
phot
ons
![Page 178: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/178.jpg)
Optimal exposure time(anomalous differences)
I-I+
3%
100
phot
ons
14 photons
100
phot
ons
![Page 179: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/179.jpg)
Optimal exposure time(anomalous differences)
3%
I-I+
2000
pho
tons
67 photons
![Page 180: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/180.jpg)
Optimal exposure time(anomalous differences)
1%
I-I+
20,0
00 p
hoto
ns
200 photons
![Page 181: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/181.jpg)
Minimum required signal (MAD/SAD)
"#
)(3.1
fsites
DaMW
sd
I
![Page 182: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/182.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 183: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/183.jpg)
“photon counting”
Read-out noise
Shutter jitter
Beam flicker
spot shape
radiation damage
σ(N) = sqrt(N)
rms 11.5 e-/pixel
rms 0.57 ms
0.15 %/√Hz
pixels? mosaicity?
B/Gray?
signal vs noise
![Page 184: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/184.jpg)
Optimal exposure time(anomalous differences)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
![Page 185: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/185.jpg)
Optimal exposure time(anomalous differences)
σtotal2 = σspot
2 + σbg2 + σreadout
2+ σraddam2
![Page 186: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/186.jpg)
Optimal exposure time(anomalous differences)
0MADt
no detector is perfectly calibrated!
σtotal2 = Nspot + σbg
2 + σreadout
2+ σraddam2
+ (fshutterNspot )2 + (fflickerNspot )2
+ (fcalibNspot )2
σtotal2 = Nspot + σbg
2 + σreadout
2+ σraddam2
![Page 187: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/187.jpg)
Fractional error
mult > (—)2Rmerge
<ΔF/F>
![Page 188: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/188.jpg)
Holton & Frankel (2010) Acta D 66 393-408.
![Page 189: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/189.jpg)
Damage model system
![Page 190: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/190.jpg)
67 consecutive data sets
![Page 191: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/191.jpg)
67 consecutive data sets
![Page 192: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/192.jpg)
Data quality vs exposure
0.5
0.55
0.6
0.65
0.7
0 20 40 60 80 100
model vs warp
Exposure time (min)
Cor
rela
tion
coef
ficie
nt
![Page 193: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/193.jpg)
Data quality vs exposure
579
1113151719212325
0 20 40 60 80 100
3A bin
Exposure time (min)
![Page 194: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/194.jpg)
Data quality vs exposure
15
17
19
21
23
25
27
29
0 20 40 60 80 100
overall
Exposure time (min)
![Page 195: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/195.jpg)
Data quality vs exposure1.7
1.9
2.1
2.3
2.5
2.7
0 20 40 60 80 100
I/sig(I) < 2
Exposure time (min)
Res
olut
ion
limit
![Page 196: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/196.jpg)
Data quality vs exposure0
0.020.040.060.080.1
0.120.140.160.180.2
0 20 40 60 80 100
3A bin
Exposure time (min)
Rsy
m
![Page 197: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/197.jpg)
Experimentally-phased map
![Page 198: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/198.jpg)
Experimentally-phased map
![Page 199: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/199.jpg)
Damage changes absorbance spectrum
0
500
1000
1500
2000
2500
3000
3500
4000
4500
50001
26
40
12
64
5
12
65
0
12
65
5
12
66
0
12
66
5
12
67
0
12
67
5
12
68
0
12
68
5
12
69
0
12
69
5
12
70
0
Photon energy (eV)
coun
ts
![Page 200: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/200.jpg)
Damage changes absorbance spectrum
0
500
1000
1500
2000
2500
3000
3500
4000
4500
50001
26
40
12
64
5
12
65
0
12
65
5
12
66
0
12
66
5
12
67
0
12
67
5
12
68
0
12
68
5
12
69
0
12
69
5
12
70
0
Photon energy (eV)
coun
ts
![Page 201: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/201.jpg)
Damage changes absorbance spectrum
0
500
1000
1500
2000
2500
3000
3500
4000
4500
50001
26
40
12
64
5
12
65
0
12
65
5
12
66
0
12
66
5
12
67
0
12
67
5
12
68
0
12
68
5
12
69
0
12
69
5
12
70
0
beforebeforeburntburnt
Photon energy (eV)
coun
ts
![Page 202: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/202.jpg)
Damage changes absorbance spectrum
0
500
1000
1500
2000
2500
3000
3500
4000
4500
50001
26
40
12
64
5
12
65
0
12
65
5
12
66
0
12
66
5
12
67
0
12
67
5
12
68
0
12
68
5
12
69
0
12
69
5
12
70
0
beforebeforeburntburnt
Photon energy (eV)
coun
ts
1
0
![Page 203: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/203.jpg)
fluorescence probe for damage
Absorbed Dose (MGy)
Fra
ctio
n u
nco
nve
rted
Wide range of decay rates seen
0.
0
0
.2
0.4
0.6
0
.8
1.0
0 50 100 150 200
Half-dose = 41.7 ± 4 MGy“GCN4” in crystal
Half-dose = 5.5 ± 0.6 MGy8 mM SeMet in NaOH
Protection factor: 660% ± 94%
![Page 204: PowerPoint File available: ~jamesh/powerpoint/ Oslo_2010.ppt](https://reader036.vdocument.in/reader036/viewer/2022062518/56649ef55503460f94c08f04/html5/thumbnails/204.jpg)
http://ucxray.berkeley.edu/~jamesh/elves
Download Elves from: