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Nd-pH5, PAPER - Coggle Diagram
Nd-pH5
Create a symbolic link
Use the terminal command: ln -s /mnt/emstorage/facility/stain-proj/ndac/ .
Relion: Import .mrc images
Job: 001
Import: *mrc
Pixel size: 3.75
Voltage: 120
Spherical abberation: 2
Amplitude contrast: 0.1
Output
81 micrographs
Manual picking
Job: 002
Particle diameter: 500
Output
979 particles picked with different orientations. Titled views not so many. A lot top/bottom, but also side views.
Extract particles
Job: 003
Particle box size (pix): 120
Re-scaled particles size(pix): No
Output
979 particles
2D classification for template
Job: 004
CTF correction: Yes
Ignore CTFs until first peak: No
Number of classes: 10
T: 2
Iterations: 25
Mask diameter (Å): 500
Image alignment: Yes (6-5-1)
2D Helical segments: No
Output
Auto-refine: Estimated accuracy angles= 2.09 degrees; offsets= 3.6375 Angstroms
CurrentResolution= 23.6842 Angstroms, which requires orientationSampling of at least 5.37313 degrees for a particle of diameter 500 Angstroms
Select classes for template
Job: 005
Output
946 particles picked.
Select 10mics to test
Job: 006
Output
210 particles picked.
Autopicking
Job: 007
Low pass filter: 20
Picking Threshold: 0.8
Inter-particle distance: 240
Output
729 particles picked.
Autopicking
Job: 008
Low pass filter: 20
Picking Threshold: 0.8
Inter-particle distance: 240
Output
5,738 particles picked.
2 more items...
Autopicking
Job: 007
Low pass filter: 20
Picking Threshold: 1
Inter-particle distance: 240
Output
680 particles picked.
Not in further use..
Autopicking
Job: 007
Low pass filter: 20
Picking Threshold: 0.8
Inter-particle distance: 230
Output
754 particles picked.
Not in further use..
PAPER
