Bug #2028
closedCTF insertion not working
0%
Description
I'm trying to run CTF estimation using the latest Appion versions, and something broken. I get this error for both ACE2 and CTFfind3.
Traceback (most recent call last):
File "/home/dlyumkis/myami/appion/bin/pyace2.py", line 23, in <module>
from appionlib.apCtf import ctfinsert
ImportError: cannot import name ctfinsert
I tried the betaversion (yesterday's), and I get this error:
File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFDatactfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 80, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 989, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 876, in CTFpowerspec
outerbound*1e10, self.apix)
File "/opt/myamisnap/lib/appionlib/apCtf/ctftools.py", line 183, in powerSpectraToOuterResolution
powerspec = trimPowerSpectraToOuterResolution(data, outerresolution, freq)
File "/opt/myamisnap/lib/appionlib/apCtf/ctftools.py", line 207, in trimPowerSpectraToOuterResolution
%(outerresolution, initmaxres))
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 57, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
- FATAL ERROR ***
Requested resolution (5.000) is not available (6.773)
Please help
Updated by Dmitry Lyumkis over 12 years ago
here is a directory:
/ami/data00/appion/12aug31c/ctf/acetwo2
Updated by Neil Voss over 12 years ago
In case 1, you are using a newer pyace2 with an older appionlib
In case 2, I am surprised it gave a fatal error. I thought I fixed that. It is related to your pixelsize of 3.39, which is larger than 2.5A.
Updated by Dmitry Lyumkis over 12 years ago
I am still getting the requested resolution error. Any chance you could check it out in the directory?
Updated by Neil Voss over 12 years ago
- Status changed from New to In Code Review
- Assignee changed from Neil Voss to Dmitry Lyumkis
try it now with fix r17097.
Updated by Neil Voss over 12 years ago
- Status changed from In Code Review to In Test
Updated by Dmitry Lyumkis over 12 years ago
- Assignee changed from Dmitry Lyumkis to Neil Voss
Ok, it is now working. These are negative stain images, so the estimation should be very good. Is this why the warnings below are using the maximum resolution (6.78 Angstroms for pixel size of 3.39)?
!!! WARNING: Requested resolution (5.000) is not available (6.773)
... Preform a rotational average and remove spikes...
PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE
... Number of available peaks is 250
mNoise Model Complete in 149.38 msec
PART 4: PEAK EXTENSION
... starting peak extension
Peak Extension Complete in 0.95 msec
... starting peak extension
Peak Extension Complete in 0.91 msec
PART 5: CTF FIT AND CONFIDENCE
1/30A - 1/10A confidence is 0.953 (overfocus 0.992)
!!! WARNING: Image is possibly over-focused
5 peak confidence is 0.952 (overfocus 0.992)
!!! WARNING: Image is possibly over-focused
PART 6: CTF RESOLUTION LIMITS
!!! WARNING: Conf did not fall below 0.80, use max res of 6.9A
!!! WARNING: Conf did not fall below 0.50, use max res of 6.9A
Resolution limit is 6.88 at 0.8 and 6.88 at 0.5
Updated by Neil Voss over 12 years ago
By mathematical law, the maximum resolution (i.e. Nyquist limit) is twice the pixel size. In your case this is 6.773A.
Updated by Dmitry Lyumkis over 12 years ago
- Status changed from In Test to Closed