I am a beginner on Cryosparc (and English is not my mother tongue)
I have some questions that will probably seem stupid to you but I would really like to understand, because I am learning by myself how the software works.
I have done the tutorial, but the tutorial seems to be very simple compared to real data.
So I have some questions, because I have to analyze data but I don’t know how to choose the parameters or what to do to optimize the resolution.
First of all, how to know if the motion correction is necessary or not? Is it from the experiment ? (because for having discussed it with someone, obviously the data I have to deal with should not have motion correction, so I guess it’s from the experiment)
How do you choose if you use CTF, CTFFIND? I didn’t understand well, obviously CTFFIND is an improvement of the basic CTF, but… How do you choose which one to use? How also, do we choose the contrast amplitude?
Is it from what we see on the image?
I understand the theory of CTF but I don’t really understand the result of the image with a CTFFIND correction, how do we know if it is “good” or not?
How do we define if we take circular or elliptical blobs? What does it change concretely?
the size of the boxes for the “blob picker” (or blob select I don’t remember) how do we determine it ? In relation to the basic size of the proteins that we study experimentally? (I don’t deal with the experimental part at all)
How do we choose which corrections to apply on the received images? How am I supposed to decide what to do concretely?
to make it simple, what parameters can I change knowing that I don’t act on the manipulation and that I just receive the raw data? (for the moment I only do the refinements that I understood via the tuto)
I don’t understand all the curves, from ab initio/homogeneous refining
What do each GSFC curve symbolize? I searched and found someone who talked about different masks etc… can you enlighten me a bit more about these masks?
What is the Fourrier space slice?
How to recognize a well resolved / well reworked image from a badly reworked image?
I don’t know if I’m clear in my questions, I know that you who seem to be all pro are very childish questions, I tried to find articles before I decide to post on the forum, but I can’t really find anything precise. The tutorial is not very precise either on understanding the “why” we are really going to do this and in what conditions.
I’m also following a little course on youtube about cryosparc, but they are very very long, I didn’t finish it.