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Hi Joey,</div>
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Thank you for the reply and suggestion. I will certainly give a try. The problem from our structure is - the highly dynamic domain that we assumed contain around 255 amino acids. To be fair, I am a bit over-ambitious to see movement on those small regions.
Needless to say that the small region is an ill-defined region (density is very poor). So I am shooting in the dark. Meaning- That small region might be degraded or fall off or high dynamics. The only supportive argument about that is in ugly dynamics is the
region lies on the active site and our enzyme is more or less active. I am not neglecting the fact that the structure we solved might be after the enzyme activity (assuming the active is lightning fast).</div>
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Have you tried to see the movement in those small regions?</div>
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Thanks</div>
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Jay</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Joey Davis <jhdavis@mit.edu><br>
<b>Sent:</b> Monday, May 25, 2020 11:17 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> Re: [3dem] About dynamics (Joey Davis)</font>
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<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>
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<div dir="ltr" class="x_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>
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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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----------------------------------------------------------------------<br>
<br>
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>
<<a href="mailto:DM6PR02MB52761A66DE2386F88BEBE6EFD0B30@DM6PR02MB5276.namprd02.prod.outlook.com" target="_blank">DM6PR02MB52761A66DE2386F88BEBE6EFD0B30@DM6PR02MB5276.namprd02.prod.outlook.com</a>><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>
Message-ID:<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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<br>
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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<div style="font-size:small">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>
Joseph H. Davis</div>
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<div style="font-size:small">Massachusetts Institute of Technology</div>
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<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>
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