Feature #1967
closed
Phase 3 Next Gen CTF Display Tools: CTF resolution
Added by Neil Voss about 12 years ago.
Updated over 11 years ago.
Category:
Python scripting
Description
My next gen tools now measure the resolution at which the CTF is no longer good at both 0.8 and 0.5 confidence.
In this update, I have changed ACE1, ACE2, Xmipp, and CTFfind to use the new ctf display tools and insert the resolution into the database.
For the next phase (#4) to come after things stabilize, I will re-write the get best defocus function to take the CTF values with the best resolution, rather than the confidence value, which is prone to false positives.
- Category set to Python scripting
- Target version set to Appion/Leginon 2.3.0
- Target version changed from Appion/Leginon 2.3.0 to Appion/Leginon 3.0.0
Hey Neil,
I've just moved all the 2.3.0 version features to 3.0, as I don't think we should release a 2.3. I'm hoping we can keep any new features to CentOS6 and therefore 3.0, but let me know if that is not possible for you.
Hi Amber,
Sorry, I had too many choices, and did not know which one to put down.
Note: that for bugs, we should have a separate option for Appion 2.2 and trunk, currently, the only choice available is "Appion 2.2 (trunk)"
Agreed. Yes, I've been trying to clean up the versions today to close out old ones and limit it to actively developed versions.
Yes, bug fixes will continue on 2.2 branch as well as in the trunk (3.0 at the moment). I'll update the label to be clear.
Neil,
Two questions and one suggestion on this feature:
1. Are you ready to release this feature or do you want to write it up before Appion official release?
2. Is it possible to scale the 2-D graph to a different resolution by user or according to the cc 0.8 result? We are using lower defocus than before on big viruses, and it is hard to see if the fit goes well when there are only one and half a node (only shown at corners) on the Thon ring.
3. There are quite some confusion about reading the 1-D graphs. Most people ask why the red line in the bottom right graph not fitting very well and do not notice that the red line is for overfocus fit at the same absolute defocus value (unless I am reading it wrong). They also fail to appreciate the graph above that shows the result of your new cc color coding. My suggestion is reversing the order of these two and highlighting the resulting bottom graphs somehow. Either make the frame thicker or put a box around them. People tend to think the bottom panel, especially bottom right panel represents the final result.
You may also consider using red for the bottom left "underfocus fitting" and another color for the "overfocus fitting" such as blue since red stands out a lot more than any other color and draws attention from people.
1. I think the CTF is ready for release.
2. The 2D graph limit is a hard-coded resolution value. I want it to be consistent, but I was unsure how to go about it, we could always show 10 rings or something else?
3. I think I can drop the overfocus check graph. I do not think I have that fine of a control over the display. As I am writing the paper in my spare time, it will get better documented.
I hope to have my manuscript ready for submission by January, which probably longer than your time frame, so do what you need to do...
- Status changed from Assigned to Closed
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