Bug #1877
closedproblems with ctfestimate.py in defocus range and display
0%
Description
Tried to run ctfestimate.py, results sometimes gave positive and sometimes gave negative defocus values.
After looking at log file, found defaulted search range is set between -74896 and 25104 which doesn't seem to make sense.
Also, I don't know how to interpret the new display. (attached)
thanks!
Logfile:
Distributed under the GNU General Public License (GPL) Input image file nameCTF DETERMINATION, V3.5 (7-March-2012)
12jun18b_c_035gr_03sq_02hl_09ed.mrc Output diagnostic file name
12jun18b_c_035gr_03sq_02hl_09ed-pow.mrc CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]
2.0 200.0 0.07 42134.8 6.000 Positive defocus values for underfocus
Box, ResMin[A], ResMax[A], dFMin[A], dFMax[A], FStep[A], dAst[A]
256 100.0 12.0 -74896.0 25104.0 2000.0 500.0 Opening MRC/CCP4 file for READ...
File : 12jun18b_c_035gr_03sq_02hl_09ed.mrc
WARNING: NO MACHINE STAMP
NX, NY, NZ: 4096 3072 1
MODE : real
Min, max : 5475.043 8719.488
Mean, RMS : 7644.072 800.0270 READING IMAGE...
NX, NY= 4096 3072 TILING IMAGE... Total tiles and number used 192 191
Lower resolution limit reset to 50.00000 A FILTERING POWER SPECTRUM... SEARCHING CTF PARAMETERS... DFMID1 DFMID2 ANGAST CC -74000.00 -74000.00 0.00 0.01626
-72000.00 -74000.00 0.00 0.02031
-72000.00 -72000.00 0.00 0.03109
-72000.00 -70000.00 0.00 0.03512
-70000.00 -70000.00 0.00 0.04296
-60000.00 -58000.00 0.00 0.04732
-48000.00 -48000.00 0.00 0.05407
-48000.00 -46000.00 0.00 0.06787
-46000.00 -46000.00 0.00 0.06946
-40000.00 -40000.00 0.00 0.07285
-40000.00 -38000.00 0.00 0.08087
-38000.00 -38000.00 0.00 0.08941
-36000.00 -38000.00 0.00 0.09699
-36000.00 -36000.00 0.00 0.10241
-34000.00 -34000.00 0.00 0.10833
-34000.00 -32000.00 0.00 0.11743
-32000.00 -32000.00 0.00 0.12775
-30000.00 -32000.00 0.00 0.14162
-30000.00 -30000.00 0.00 0.15800
-28000.00 -30000.00 0.00 0.16059
-28000.00 -28000.00 0.00 0.17366
-26000.00 -28000.00 0.00 0.17690
-28000.00 -26000.00 0.00 0.17762
-26000.00 -26000.00 0.00 0.19700
-24000.00 -26000.00 0.00 0.19987
24000.00 24000.00 0.00 0.22364 REFINING CTF PARAMETERS... DFMID1 DFMID2 ANGAST CC 24191.66 24551.64 20.55 0.22593 Final Values Opening MRC/CCP4 file for WRITE...
File : 12jun18b_c_035gr_03sq_02hl_09ed-pow.mrc
NX, NY, NZ: 256 256 1
MODE : real
Files
Updated by Neil Voss over 12 years ago
Can I see the parameters that were passed to ctfestimate?
Updated by Neil Voss over 12 years ago
- Status changed from New to Assigned
- Assignee changed from Neil Voss to Melody Campbell
- Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0 (trunk)
Updated by Melody Campbell over 12 years ago
Yes, here's what I put in:
ctfestimate.py --projectid=365 --preset=ed --session=12jun18b --runname=ctffindrun42135a --rundir=/ami/data00/appion/12jun18b/ctf/ctffindrun42135a --no-rejects --no-wait --commit --continue --ampcarbon=0.15 --ampice=0.07 --fieldsize=256 --medium=ice --bin=1 --resmin=100.0 --resmax=12.0 --defstep=2000.0 --dast=500 --expId=10075 --jobtype=ctfestimate
Updated by Melody Campbell over 12 years ago
- Assignee changed from Melody Campbell to Neil Voss
Updated by Neil Voss over 12 years ago
Hi Melody,
Okay, I found the bug, it should be fixed in r16833.
Also, it looks like you were using the old webpage for the newer python script. But it should be backwards/forwards compatible. Read Feature #1867 for more details.
On the interpretation, it would be more obvious if your image had any Thon rings. The picture is the power spectra of the micrograph, and the blue lines are the fitted CTF Thon rings. Read Feature #1847 for more details.
Updated by Neil Voss over 12 years ago
- Status changed from Assigned to In Test
- Assignee changed from Neil Voss to Melody Campbell
Updated by Melody Campbell over 10 years ago
- Status changed from In Test to Closed
- Affected Version changed from Appion/Leginon 2.2.0 (trunk) to Appion/Leginon 2.2.0