Re: [scipion-users] HEMNMA visualization and nma-align efficiency

[Carlos O. S. <co...@cn...>]

Dear Lizelle,


I am forwarding your mail to Slavica, who is the person in charge of 
ContinuousFlex.


Kind regards, Carlos Oscar


El 24/11/2021 a las 15:58, Lizelle Lubbe via scipion-users escribió:
> Hi everyone,
>
> I would like to run HEMNMA on my particles and have done the NMA step 
> using an atomic model. Is there any way to visualize the trajectories 
> other than through VMD in Scipion? I am accessing the campus computer 
> with Scipion remotely and it seems like VMD installation may be an issue.
>
> Three modes from an input PDB show high collectivity with low scores 
> and I would like to now try NMA alignment with these modes. Given the 
> high computational cost of the protocol, is it recommended to use a 
> subset of particles for the analysis at present? The original stack is 
> of ~100k particles (discrete heterogeneity was removed by 2 rounds of 
> 2D classification and some 3D classifications but there is still 
> continuous heterogeneity). It would be great to see the full range of 
> variations with all particles but maybe not computationally feasible 
> at present? The box size at 1.06A/pix is 256 so I can maybe bin by 4 
> to 64pix but windowing further will cut into my particle.
> We have 256GB RAM with 24 Intel(R) Xeon(R) Silver 4214R CPU @ 2.40GHz 
> and 4 Quadro RTX 5000 GPUs.
>
> Kind regards,
> Lizelle
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