Hello All,
I have a few questions relating to 3D Classification and Align 3D jobs.
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What does performing 3D classification with 2 map inputs achieve? Does it just redistribute the particles into one of these 2 classes? If I understand correctly, then running it with 1 map does nothing since it would output 1 class.
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I was thinking of running 3D classification with 2 input maps of my protein. One of them is an octamer and the other is a nonamer, but they’re both rings that are made of the same repeating subunit.
- In this case, a solvent/focus mask covering one would not be a good fit for the other. Where could I take it from here?
- I was thinking that since, according to my understanding, I have to run an Align 3D job to align them before doing that, maybe I can align both proteins in a way where one subunit is perfectly aligned and have the focus mask be on that region, but I’m not sure how to achieve this, or if it is reasonable. What would I do/what masks would I use in the Align 3D or the 3D Classification job to achieve this?
- I am having trouble deciding what the different types of mask inputs do in the Align 3D job, i.e. What does a reference mask do in comparison with “Mask (map to align, connection 1)” and what does “create mask inputs do”. I read through the tutorial for the job, but I don’t really understand it. Why would I need to use either of these options or both?
I apologize if any of these questions are silly, but I’m really struggling to understand these jobs and what the masks do. Thank you in advance.
Kind regards,