Please enable JavaScript.
Coggle requires JavaScript to display documents.
20180207-EGTA (Extract/job110 Input: BestCtf.star (excluded micrograph…
20180207-EGTA
Extract/job110
Input: BestCtf.star (excluded micrograph 285 with resolution of 11 using edit &)
script input: cleaned manual pick :)
Autopick/job014/coords_suffix_autopick.star
Class2D/job123
Select/job127
284,252 particles
Class3D/job152
C2 symmetry
Class3D/job153
C1 symmetry
Class3D/job118/
C2 symmetry
Ignore 1st peak? no
Class 1: 9.2% 17.4 A
Class 2: 10.1% 15.47 A
Class 3: 9.5% 16.38 A
Class 4: 7.5% 15.47 A
Class 5: 2.6% 16.38 A
Class 6: 12.2% 13.26 A
Class 7: 15.2% 16.38 A
Class 8: 13.0% 12.10 A
Class 9: 11.9% 13.26 A
Class 10: 8.8% 17.41 A
Select/job130
Refine3D/job132
19.89 A
ref: class004.mrc
Refine3D/job133
class 6
9.95 A
ref: class006.mrc
Refine3D/job131
class 1
19.89 A
ref: class001.mrc
Refine3D/job134
class 7
21.43 A
ref: class007.mrc
Refine3D/job135
class 8
10.32 A
ref: class008.mrc
Refine3D/job136
class 9
13.26 A
ref: class009.mrc
good classes only
Refine3D/job151
classes 14689
ref: merged-apo.mrc
Ignore CTF? no
9.6 A
Class3D/job138
10 classes
Class 7: 18.99% 11.14 A
Select/job144
30,297 particles
Refine3D/job155
class 7
ref: class007.mrc
8.704 A
same as class 2 of Class3D/job173
**
Extract/job243
384x384 pixel box
1.088 Å
30,297 particles
Extract/job243
256x256 box
1.088 Å
30,297 particles
Refine3D/job245
C2 Symmetry
8.7 Å
1 more item...
Refine3D/job197
class 7
ref: class007.mrc
reference mask: 3x3Mask.mrc
Refine3D/job199
same as Refine3D/job197
200 A instead of 150 A
Link Title
Class3D/job204
same as Class3D/job138
use 100 A instead of 200 A
all classes
Refine3D/job137
10.71 A
ref: merged_apo
Class3D/job125
C2 symmetry
Ignore 1st peak? no
perform image alignment? NO
don't do this until refinement
Class3D/job139
C2 symmetry
Ignore 1st peak? yes
CtfFind/job02
max resolution 5
512 pix
ManualPick/job003
207 particles
(cleaned out bad CTF)
AutoPick/job014
threshold 0.4
Extract/job018
308,149 particles
binned 2
Class3D/job039
C2 symmetry
6 classes
Ignore 1st peak? Y
Class2D/job021
100 classes
Select/job023
296,518 particles
Class2D/job024
Select/job027
280,627 particles
Class3D/job030
10 classes
C2 symmetry
Ignore 1st peak? Y
ref: merged_apo
Class3D/job022
C2 symmetry
10 classes
perform alignment? Y
Class 1: 17% 12.10A
Class 2: 8.4% 18.56 A
Class 3: 9.6% 18.56 A
Class 4: 7.5% 15.47 A
Class 5: 8.3% 17.4 A
Class 6: 4.4% 17.4 A
Class 7: 8.07% 16.38 A
Class 8: 15.1% 17.4 A
Class 9: 9.4% 17.4 A
Class 10: 11.9% 15.47 A
Select/job025
Refine3D/job032
class 10
13.9 A
36,475 particles
ref: class010.mrc
Class3D/job048
3 classes
Ignore 1st peak? Y
Refine3D/job082
13.93 A
Refine/job083
17.41 A
Refine3D/job081
17.41 A
Refine3D/job035
class 8
19.9 A
46,497 particles
ref: class008.mrc
Class3D/job047
3 classes
Ignore 1st peak?
Refine3D/job031
class 4
14.6 A
23,241 particles
ref: class004.mrc
Class3D/job046
3 classes
Ignore 1st peak? Y
Refine3D/job036
class 1
53,100 particles
9.6 A
ref: class001.mrc
Class3D/job045
ref: class001
3 classes
Ignore 1st peak? Y
Refine3D/job073
class 1
9.28 A
ref: class001
Refine3D/job076
classes 1+3
8.44 A
ref: class001
Refine3D/job074
class 3
10.32 A
ref: class003
Refine3D/job120
all classes
11.14 A
ref: class001.mrc
Refine3D/job034
classes 1+4+10
8.44 A
89,575 particles
ref: class001.mrc
Class3D/job163
mask: 120
no image alignment
ref: job034_class001.mrc
Class3D/161
mask: 200
no image alignment
ref:job034_class001.mrc
Class3D/job173
mask:100
no image alignment
ref:job034_class001.mrc
23%, 18.5%, 24.2%, 18.55%, 15.57%
9.28, 8.19, 9.28, 9.28, 8.98
Select/job174
class 2 - 11,712
class 3 - 9.832
classes 2+5 - 21,544
7 more items...
Class3D/job179
diameter: 80 A
(cuts the voltage domain)
ref: Refine3D/job034/class001.mrc
Class3D/job183
diameter: 100 A
masks the micelles perfectly! (120A is too liberal)
ref: Refine3D/job034/class001.mrc
with mask-TMD (made from class 2 of Class3D/job173)
Class 1: 19% 8.19 A
Class 2: 21.7% 8.19 A
Class 3: 19.5% 8.44 A
Class 4: 21.7% 8.70 A
Class 5: 17.5% 8.19 A
Class3D/job181
diameter: 100 A
ref: Refine3D/job034/class001.mrc
with full mask (made from 2 of Class3D/job173)
63,011 particles
Class 1: 17.4% 8.44 A
Class 2: 18.7% 8.44 A
Class 3: 23.0% 8.44 A
Class 4: 16.97% 7.96 A (10,705 particles)
Class 5: 24.0% 8.44 A
1 more item...
Refine3D/job206
ref: job173/class002.mrc
mask: 3x3mask.mrc
100A masking diameter
10.71 A
Select/job205
class 4
63,011 particles
1 more item...
Refine3D/job208
Select 1410
mask: full 3x3
200 A diameter
7.14 A without masking
Class3D/job038
C1 symmetry
Ignore 1st peak? Y
some micelles are uniform and square while others are lopsided (try changing detergent conditions)
Select/job097
classes 4 and 8 look good (tdisp)
4 more items...
Class3D/job218
ref: cisTEM_job246_128.mrc
mask: cisTEM_job246_nomicelle_128_3x3.mrc
Extract/job042
Re-extract from Refine3D/job026
for cisTEM (no binning)
refine package #2
Extract/job084
cleaned micrographs
Class3D/job091
C2 symmetry
Ignore 1st peak? Y
Image alignment? Y
Class3D/job092
C1 symmetry
Ignore 1st peak? Y
Image alignment? Y
Class2D/job086
Ignore 1st peak? Y
Image alignment? N
Class3D/job095
C1 symmetry
Ignore 1st peak? Y
Image alignment? N
Class2D/job085
Ignore 1st peak? Y
Select/job104
Class3D/job096
C2 symmetry
Ignore 1st peak? Y
Image alignment? N
cisTEM refine package #3
Extract/job241 - 291,1593 particles 384x384->192x192 box size
Combined with 116,483 particles from
Extract/job085/ in 20180126-EGTA
JoinStar/job003 Combine of Extract/job085/particles.star and Extract/job241/particles.star
408,076 particles
Class2d/job004 10,000 subsets for initial iterations
100 classes
25 iterations
160A Mask
Class2d/job004
No subsets for initial iterations
100 classes
25 iterations
160A Mask
100 mM NaCl
(better contrast in lower defocus)
1601 micrographs
CtfFind/job106
max resolution 4
10214 pix
CtfFind/job107
max resolution 7
10214 pix
