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

[Lizelle L. <liz...@uc...>]

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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