e2gmm_refine

[Jacob Croft]

Hello,

I was wondering if e2gmm_refine can be used on spt refinements or if it is only set up to work with single particle? I have eman/2.99.67 installed.

Best,

Jake Croft

[Muyuan Chen]

Both the orientation refinement and the heterogeneity analysis for SPT has been working for a while. I just never made the effort to write a specific paper about it... A short documentation here. 

https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_p22#GMM-based_refinement

It is better to build from source to get the latest updates. There are also a few other programs named e2gmm_spt_xxx.py for various purposes. Probably should write something about them but never get the motivation...

Muyuan

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[Jacob Croft]

Thank you for pointing me to the documentation Muyuan.  Could you help me understand what the seg.pdb file output from e2_gmm_guess_n is? The documentation says it can be used to visualize the coordinates of the gaussians in the density map, so I was expecting it to look like a bunch of spheres, but when I opened it up in chimera it looks like a tangle of spaghetti. Is this a problem with how I am visualizing it?

Best,

Jake

[Muyuan Chen]

Yes it is a visualization issue. If you open it in Chimera, it always tries to connect them with loops. Just show atoms as spheres and hide cartoon would work I think. The scaling may also be wrong because the PDB format have trouble with large numbers. You will need to set pixel size of the corresponding map to 1 if you want to overlay the two. 

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