<div dir="ltr"><div>Hi Jay,</div><div><br></div><div>In addition to cryoSPARC's 3DVA and Relion's multibody, I encourage you to try
cryoDRGN, which we recently released. CryoDRGN's methods and underlying
assumptions are quite different from those of cryoSPARC/Relion, and we've seen it work well with a variety of both discrete and continuously heterogeneous systems. You can find a preprint describing the approach here: <a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61fc6FSoCg$" target="_blank">https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1</a>, and the source code/installation instructions/usage guide here: <a href="https://urldefense.com/v3/__https://github.com/zhonge/cryodrgn__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61ctRUs-Fg$" target="_blank">https://github.com/zhonge/cryodrgn</a>. </div><div><br></div><div>Please let me know if you have any questions - happy to help.</div><div><br></div><div>Best of luck,</div><div>Joey</div><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br></div><div dir="ltr" class="gmail_attr">On Mon, May 25, 2020 at 9:34 PM <<a href="mailto:3dem-request@ncmir.ucsd.edu" target="_blank">3dem-request@ncmir.ucsd.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send 3dem mailing list submissions to<br>
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Today's Topics:<br>
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1. About dynamics (Jay Rai)<br>
2. Re: About dynamics (Jay Rai)<br>
3. Re: About dynamics (Ali Punjani)<br>
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Message: 1<br>
Date: Mon, 25 May 2020 19:27:35 +0000<br>
From: Jay Rai <<a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>><br>
To: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
Subject: [3dem] About dynamics<br>
Message-ID:<br>
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<br>
Dear Cryo-EM folks,<br>
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.<br>
Thanks<br>
Jay<br>
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Message: 2<br>
Date: Tue, 26 May 2020 00:03:55 +0000<br>
From: Jay Rai <<a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>><br>
To: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
Subject: Re: [3dem] About dynamics<br>
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<br>
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?<br>
Thanking you in advance,<br>
jay<br>
________________________________<br>
From: 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" target="_blank">3dem-bounces@ncmir.ucsd.edu</a>> on behalf of Jay Rai <<a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>><br>
Sent: Monday, May 25, 2020 3:27 PM<br>
To: <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
Subject: [3dem] About dynamics<br>
<br>
Dear Cryo-EM folks,<br>
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.<br>
Thanks<br>
Jay<br>
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Message: 3<br>
Date: Mon, 25 May 2020 21:33:14 -0400<br>
From: Ali Punjani <<a href="mailto:alipunjani@cs.toronto.edu" target="_blank">alipunjani@cs.toronto.edu</a>><br>
To: Jay Rai <<a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>><br>
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
Subject: Re: [3dem] About dynamics<br>
Message-ID:<br>
<CAP_b-V-F+w14=<a href="mailto:sLYQY9fWW6tCfc6ggKg-GPGcWwum86%2BW7Vh8Q@mail.gmail.com" target="_blank">sLYQY9fWW6tCfc6ggKg-GPGcWwum86+W7Vh8Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Jay,<br>
<br>
In cryoSPARC, you can try the new 3D Variability Analysis (3DVA) algorithm<br>
that can directly resolve continuous heterogeneity and flexibility from<br>
single particle data. We've recently written a paper about the algorithm<br>
and how to interpret results (preprint:<br>
<a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.04.08.032466v1__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQiqEm9CQ$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.04.08.032466v1__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQiqEm9CQ$</a> ) and there are<br>
a couple of detailed tutorials online as well (<br>
<a href="https://urldefense.com/v3/__https://cryosparc.com/docs/tutorials/3d-variability-analysis__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQykYwUEg$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://cryosparc.com/docs/tutorials/3d-variability-analysis__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xQykYwUEg$</a> ). The<br>
algorithm has been used in several published studies to date and can<br>
resolve flexible dynamics even for smaller proteins eg. GPCR complexes.<br>
You may also be interested in related discussions ongoing on the cryoSPARC<br>
discussion forum (<a href="https://urldefense.com/v3/__https://discuss.cryosparc.com/__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xR2x7wM2Q$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__https://discuss.cryosparc.com/__;!!Mih3wA!TcYCUD_wBUr5IORGTt-uKmJtnjAN7is2w2qHfWKXW5ewtmxRcaG0CfJN6xR2x7wM2Q$</a> ).<br>
<br>
Thanks,<br>
Ali Punjani<br>
<br>
<br>
On Mon, May 25, 2020 at 8:04 PM Jay Rai <<a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>> wrote:<br>
<br>
> Just to be add: Its work like a charm on big complexes like ribosome. In<br>
> other words- which software is best for the multibody refinement/ protein<br>
> dynamics?<br>
> Thanking you in advance,<br>
> jay<br>
> ------------------------------<br>
> *From:* 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" target="_blank">3dem-bounces@ncmir.ucsd.edu</a>> on behalf of Jay Rai <<br>
> <a href="mailto:jrai@fsu.edu" target="_blank">jrai@fsu.edu</a>><br>
> *Sent:* Monday, May 25, 2020 3:27 PM<br>
> *To:* <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>><br>
> *Subject:* [3dem] About dynamics<br>
><br>
> Dear Cryo-EM folks,<br>
> I am trying to solve the dynamics of 300 kD multi proteins complex. Any<br>
> idea which software is the most useful? Any tips and suggestions. So, far I<br>
> tried Relion and cryosprac. Both gave me different results.<br>
> Thanks<br>
> Jay<br>
> _______________________________________________<br>
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><br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div style="font-size:small">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>Joseph H. Davis</div><div style="font-size:small">Whitehead Career Development Assistant Professor of Biology</div><div style="font-size:small">Massachusetts Institute of Technology</div><div style="font-size:small">77 Massachusetts Ave.</div><div style="font-size:small">68-671A</div><div style="font-size:small">Cambridge, MA 02139</div><div style="font-size:small">617.258.6154</div><div style="font-size:small"><a href="https://urldefense.com/v3/__http://www.jhdavislab.org__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61e1p_IRFg$" target="_blank">www.jhdavislab.org</a></div><div style="font-size:small">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br></div></div></div></div></div></div></div></div>