Comments and questions about defocus determination with ctffind3 and ctftilt.
Hello Dr. Grigorieff!
I'm expecting my pictures to be about 1um underfoucs. And yet the output numbers indicate that they are at most, 100nm underfocus.
Does it make a difference to ctffind that the mrc file it analyzes was originally a tif file?
Since the scanner I'm using cannot save the scanned image in mrc format, I saved it as a tif first; then I used ImageJ to convert that tif file into .mrc format.
Hello!
I was wondering how I would determine the pixel resolution for the scanner I used - Dstep input parameter?
Is there a method mentioned in a paper or outlined somewhere?
Thanks!
My question regards the output I get from ctffind3:
In your paper titled "Accurate determination of local defocus and specimen tilt in electron microscopy," the two defocus values computed by ctffind for image b3730 (given in Table 1) are said to be 597.5 nm and 525.1 nm. Using ctffind3.exe I entered the exact parameters described in page 339 of that paper, and I can't seem to make sense of the output I get.
For CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]
I entered
2.0, 200.0, 0.07, 60000.0, 7.5
It does not make any difference in practice, but just for mathematical
accuracy, I think the following line in ctffind3.f
WL=12.3/SQRT(KV+KV**2/(10.0**6.0)) ! Angstroms
should be
WL=12.26/SQRT(KV+0.9784*KV**2/(10.0**6.0)) ! Angstroms
I am interested in using the ctffind software available on your website.
Is there a list of instructions available on how to use and compile this software?
I am also planning on doing phase flipping with XMIPP, will the output file be read by this software?
