Can't generate 3D Flex mesh properly

Currently with cryosparc v4.1.2, I’m having trouble with the 3D flex mesh prep job, because as you can see in the pictures, the mesh isn’t generated properly. I only put the consensus volume from 3D flex data prep job as input, and all the parameters of both jobs are left as default. The pixel size of the original data is 0.788Å and the box size is 300px.

Please let me know if you have any solutions.

スクリーンショット 2023-01-31 11.03.43

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it’s likely the threshold. you have to open the volume in chimera, and decide on an appropriate threshold (where it looks most representative of your complex - not too swollen, but dense enough to have appropriate connectivity). Then use this number and make decisions about mask dilation and padding. probably 6 and 6 is a good start for those parameters based on your values above. but the threshold you have to see for yourself.


It worked!
Thanks for your quick reply, very helpful.

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