[3dem] CryoSPARC v4.1 Beta now available, featuring 3DFlex, cryosparc-tools, and more

[Ali Punjani]

Dear 3DEM,

We are excited to announce that 3D Flexible Refinement (3DFlex) is
available in CryoSPARC v4.1 Beta released today, December 12, 2022.

3DFlex is a motion-based deep generative model for continuous
heterogeneity. It models non-rigid motion and flexibility of a protein
molecule across its conformational landscape, and can use the motion model
to combine signal from particle images in different conformations to
improve refinement resolution in flexible regions. An in-depth tutorial,
video, new example results, and discussion of considerations and
limitations are available in the CryoSPARC Guide
<https://urldefense.com/v3/__https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/tutorial-3d-flexible-refinement__;!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HJKCb7a2$ >.
A bioRxiv preprint is online
<https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2021.04.22.440893v1__;!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HLCQmD_r$ > and an
updated paper is coming soon.

CryoSPARC v4.1 also features cryosparc-tools (BETA), a new open-source
Python library that enables powerful scripting access to CryoSPARC.
cryosparc-tools can be used to read and write exposure, particle and volume
data, perform advanced operations on metadata (e.g., alignments, CTF,
etc.), programmatically insert modified data back into CryoSPARC, build and
run jobs to orchestrate custom workflows, and extend CryoSPARC
functionality with third-party software packages. cryosparc-tools is on
Github <https://urldefense.com/v3/__https://github.com/cryoem-uoft/cryosparc-tools__;!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HDgEoFQl$ > and available via
`pip`. It can be used outside of the CryoSPARC environment in your own
programs and tools. The full documentation and example use cases are
available at https://urldefense.com/v3/__https://tools.cryosparc.com__;!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HOOzfayq$ .

The update also includes many enhancements and improvements across the
workflow and UI. For the full list of what’s new in v4.1 and all associated
documentation, please see cryosparc.com/updates.

CryoSPARC v4.0 was initially released in beta on October 3, 2022 and has
been followed by several updates. We look forward to the stable release of
v4 early in the new year.

Thank you!
The CryoSPARC Team <https://urldefense.com/v3/__https://structura.bio/*team__;Iw!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HNVQAn6e$ >
Structura Biotechnology Inc. <https://urldefense.com/v3/__https://structura.bio/__;!!Mih3wA!BvB-tIg22Y8k2cOkaa81yTaXXp8COBBKIoQOJ-STgPEliiBXf5lviVY8WI0nAN150lj_2eR4DLEGH4lTKh22HOImfriT$ >
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