[3dem] About dynamics (Joey Davis)

Mon May 25 20:17:58 PDT 2020

Hi Jay,

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: https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2020.03.27.003871v1__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61fc6FSoCg$ , and the
source code/installation instructions/usage guide here:
https://urldefense.com/v3/__https://github.com/zhonge/cryodrgn__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61ctRUs-Fg$ .

Please let me know if you have any questions - happy to help.

Best of luck,
Joey

On Mon, May 25, 2020 at 9:34 PM <3dem-request at ncmir.ucsd.edu> wrote:

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>    1. About dynamics (Jay Rai)
>    2. Re: About dynamics (Jay Rai)
>    3. Re: About dynamics (Ali Punjani)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 25 May 2020 19:27:35 +0000
> From: Jay Rai <jrai at fsu.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] About dynamics
> Message-ID:
>         <
> DM6PR02MB52761A66DE2386F88BEBE6EFD0B30 at DM6PR02MB5276.namprd02.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
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> Message: 2
> Date: Tue, 26 May 2020 00:03:55 +0000
> From: Jay Rai <jrai at fsu.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] About dynamics
> Message-ID:
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>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200526/e34fa09b/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 3
> Date: Mon, 25 May 2020 21:33:14 -0400
> From: Ali Punjani <alipunjani at cs.toronto.edu>
> To: Jay Rai <jrai at fsu.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] About dynamics
> Message-ID:
>         <CAP_b-V-F+w14=
> sLYQY9fWW6tCfc6ggKg-GPGcWwum86+W7Vh8Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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
> >
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Joseph H. Davis
Whitehead Career Development Assistant Professor of Biology
Massachusetts Institute of Technology
77 Massachusetts Ave.
68-671A
Cambridge, MA 02139
617.258.6154
https://urldefense.com/v3/__http://www.jhdavislab.org__;!!Mih3wA!WnEgFrgDg5fKSyjiE4f9IMamoJw2YDKQq2Q2O_hetUnwA2m35nlRYPWK61e1p_IRFg$ 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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