[3dem] About dynamics

[Ali Punjani]

Hi Jay,

In cryoSPARC, you can try the new 3D Variability Analysis (3DVA) algorithm
that can directly resolve continuous heterogeneity and flexibility from
single particle data. We've recently written a paper about the algorithm
and how to interpret results (preprint:
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.04.08.032466v1__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQiqEm9CQ$ ) and there are
a couple of detailed tutorials online as well (
https://urldefense.com/v3/__https://cryosparc.com/docs/tutorials/3d-variability-analysis__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQykYwUEg$ ). The
algorithm has been used in several published studies to date and can
resolve flexible dynamics even for smaller proteins eg. GPCR complexes.
You may also be interested in related discussions ongoing on the cryoSPARC
discussion forum (https://urldefense.com/v3/__https://discuss.cryosparc.com/__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xR2x7wM2Q$ ).

Thanks,
Ali Punjani


On Mon, May 25, 2020 at 8:04 PM Jay Rai <jrai at fsu.edu> wrote:

> Just to be add: Its work like a charm on big complexes like ribosome. In
> other words- which software is best for the multibody refinement/ protein
> dynamics?
> Thanking you in advance,
> jay
> ------------------------------
> *From:* 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Jay Rai <
> jrai at fsu.edu>
> *Sent:* Monday, May 25, 2020 3:27 PM
> *To:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> *Subject:* [3dem] About dynamics
>
> Dear Cryo-EM folks,
> I am trying to solve the dynamics of  300 kD multi proteins complex. Any
> idea which software is the most useful? Any tips and suggestions. So, far I
> tried Relion and cryosprac. Both gave me different results.
> Thanks
> Jay
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200525/ba115218/attachment-0001.html>