CTF estimation on Cs-corrected images
Added by Michael Cianfrocco over 10 years ago
Hello,
We recently collected data on a Titan Krios (at Janelia Farm) that is Cs-corrected. Unfortunately, appion won't let us upload images with a Cs = 0 mm at the uploadimage.php webpage.
Two questions:
1) What do you think appion would do if we manually entered 0 into the command line uploader script?
2) Is there a way to change this web page to allow for Cs-correct images to be uploaded?
thanks!
mike
Appion version: 3.0
Revision #: 18213
Replies (6)
RE: CTF estimation on Cs-corrected images - Added by Amber Herold over 10 years ago
Hi Mike,
I'll go ahead and change the code so that cs = 0 is valid.
If you just change the command line value, the python script will check that the cs value is at least 0.1.
I'll let you know when I have checked in the changes to the GUI and Python script to the 3.0 branch.
Amber
RE: CTF estimation on Cs-corrected images - Added by Michael Cianfrocco over 10 years ago
Thanks Amber!
In addition to the problem of uploading images, we also noticed that if you put in very small Cs values (e.g. Cs = 0.1), the CTF estimation script would flag the all the micrographs and not create a diagnostic image:
WARNING atypical Cs value 0.1 mm WARNING Bad CTF values insert but not create images
Is it possible to also update the ctf estimation to output a diagnostic image?
RE: CTF estimation on Cs-corrected images - Added by Amber Herold over 10 years ago
Will take a look...
RE: CTF estimation on Cs-corrected images - Added by Amber Herold over 10 years ago
Alright, both issues should be corrected with #2762.
Please give it a try and let me know how it goes.
RE: CTF estimation on Cs-corrected images - Added by Amber Herold over 10 years ago
Opps, just saw your update to the issue, let me look at that before trying again..
RE: CTF estimation on Cs-corrected images - Added by Michael Cianfrocco over 10 years ago
Hi Amber,
I got around that problem I posted to the issues page, but now i'm getting an error:
==== Committing data to database ====
... Committing ctf parameters for 14may07z_14apr11z_A1_49k_1 to database
!!! WARNING: |def1| > |def2|, flipping defocus axes
... Reading image...
[CTF param] def1: 6.37e-07 | def2: 6.89e-07 | angle: -74.1 | ampcontr 0.15 | defratio 1.082
Traceback (most recent call last):
File "/labdata/allab/michaelc/myami-3.0-trunk//appion/bin/ctfestimate.py", line 421, in <module>
imgLoop.run()
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 97, in run
self.loopCommitToDatabase(imgdata)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 146, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/labdata/allab/michaelc/myami-3.0-trunk//appion/bin/ctfestimate.py", line 329, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctfinsert.py", line 80, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 1120, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 972, in CTFpowerspec
self.convertDefociToConvention(ctfdata)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 916, in convertDefociToConvention
self.initfreq, self.cs, self.volts, self.ampcontrast)
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctftools.py", line 162, in defocusRatioToEllipseRatio
cs, volts, ampcontrast, numzeros=1, zerotype="valleys")
File "/labdata/allab/michaelc/myami-3.0-trunk/myami/lib/python2.6/site-packages/appionlib/apCtf/ctftools.py", line 71, in getCtfExtrema
radsq1 = (-b + root)/(2*a)
ZeroDivisionError: float division
It looks like Cs=0 results in an equation that tries to divide by zero.
Sorry to keep troubling you with this.
mike