Re: [scipion-users] New plugin scipion-em-prody extending protein dynamics capabilities

[Dmitry S. <sem...@gm...>]

hello James,

Great news.

Thank you!

Kind regards, 
Dmitry


> On 19. Apr 2022, at 13:36, James Krieger <jam...@gm...> wrote:
> 
> Dear all,
> 
> I am pleased to announce that we now have the first working version of the scipion-em-prody plugin (v3.0.3), linking Scipion to the ProDy Python package (v2.1.1) for protein dynamics analysis (http://prody.csb.pitt.edu/ <http://prody.csb.pitt.edu/>). 
> 
> So far, we have protocols and viewers for the following tasks:
> - atom selection (using VMD-like commands as described at http://prody.csb.pitt.edu/manual/reference/atomic/select.html <http://prody.csb.pitt.edu/manual/reference/atomic/select.html>) 
> - atomic structure alignment based on Biopython sequence alignment and sequence- and structure-based chain matching
> - anisotropic network model (ANM) normal mode analysis (NMA)
> - deformation vector analysis for calculating transitions/differences between two structures
> - motion visualisation with the VMD normal mode wizard (NMWiz)
> - mode/vector editing tools to account for different numbers of atoms including residue-based slicing and extending, as well as the more physically meaningful Hessian reduction for vibrational-subsystem analysis 
> - importing of normal modes in Scipion format, the two main ProDy formats (nmd and npz), and Gromacs format
> 
> You can see examples of these protocols in the test pipeline.
> 
> Look out for more exciting tools, protocols and pipelines soon including Gaussian network model (GNM) analysis and ClustENM hybrid simulations!
> 
> Best wishes
> James
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