Graph traversal movies #79
Guillawme
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Hello there, The release of this dataset took a very long time because I made a mistake with the deposition (I included files EMPIAR did not expect). But in case somebody wants to play with cryoDRGN on this dataset, it is now finally available: https://www.ebi.ac.uk/empiar/EMPIAR-10739 In this deposition, there are three sets of extracted particles:
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Hello,
I am posting here some pointers about making a movie from a graph or principal component traversal. This was discussed in an issue (#63) before we started using "Discussions", but it will have more visibility here than in the middle of bug reports.
Back in June, @EB-kim asked:
At this time, I was just in the middle of making such movies for an article that was almost ready for submission, so I shared the following minimal example (a ChimeraX command file):
The article I was making movies for is now published, so I posted my scripts in this repository and you can see the corresponding movies here. This should complement well the generic example above.
Here are the steps I followed to generate the animated UMAP plot in the graph traversal movie, only using free/open-source software:
cryodrgn analyze
to make it plot a red dot at the coordinate of each reconstruction in the volume series and save each plot as a PNG fileffmpeg
to assemble all these PNG files into an animation with the same frame rate as the volume series movie from ChimeraX (not only the same frame rate, but also the same "step rate" through the volume series and the corresponding UMAP coordinate series, so that the next dot on the UMAP plot would appear at the same time as the next map in the volume series)I hope this helps!
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