Appion

Neil, Please work on this asap. I really want to merge your ctf stuff to myami-beta but I can not do so until it works right. It might be as simple as a problem of plot scale. As you can see, and I observed on other plots that the minimum in Y is 1.0, not 0.0 which I assume it should be.

Works now, I had to adjust the parameters which floors the data.

Neil,

3d4e2a6b further changes this. I have many images from K2 camera that end up with flat line from the last commit. This new change at least make it a bit better. These images have normexprotdata maximum smaller or close to 1.0.

The result of this commit still gives the first section envelop (magenta) line away from the data (blue) and fit(green) in the example attached. Therefore, I might still missed something. Hope you can find out where.

For other testing, try the appion testdata set of GroEL images. I can also give you more images of this type or phase plate images which are usually -0.5 um defocus and with large values at low resolution.

An example is attached.
ctffind4 result

# Output from CTFFind version 4.1.5, run on 2016-10-05 15:19:28
# Input file: 16oct04c_a_050gr_012sq_06hl_04ex-a.mrc ; Number of micrographs: 1
# Pixel size: 0.900 Angstroms ; acceleration voltage: 300.0 keV ; spherical aber
ration: 2.20 mm ; amplitude contrast: 0.07
# Box size: 1024 pixels ; min. res.: 50.0 Angstroms ; max. res.: 3.0 Angstroms ;
 min. def.: 1000.0 um; max. def. 46929.8 um
# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #
4 - azimuth of astigmatism; #5 - additional phase shift [radians]; #6 - cross co
rrelation; #7 - spacing (in Angstroms) up to which CTF rings were fit successful
ly
1.000000 22435.417969 21929.798828 73.746925 0.000000 0.019749 6.433184

Appion input

ctffind4.py   --ampcontrast=0.07 --fieldsize=1024 --resmin=50 --resmax=3 --defstep=0.1   --numstep=25 --dast=0.05 --best-images --min_phase_shift=10   --max_phase_shift=170 --phase_search_step=10 --runname=ctffind4run4   --rundir=/nis/ucsd-02/appion/16oct04c/ctf/ctffind4run4 --preset=ex-a   --commit --projectid=4 --session=16oct04c --no-rejects --no-continue   --expid=19 --jobtype=ctfestimate --no-wai

these changes look good.