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Dear Chan,

Alignment of particles seems to me as a very vague term.
1. Alignment for what? 2D classification?
If that is the case, there are multiple softwares like Relion as you mentioned. Relion takes a huge computational resources if your dataset is huge and you don't have any GPU for your calculations.
2. Alignment with respect to what? Are you trying to understand your dataset for some particular interest? Or trying to focus on some particular details?

I think in both of the cases IMAGIC holds the most accurate toolsets for you. You can try this software package (https://www.imagescience.de/imagic.html) to deal with your dataset. It's fast and doesn't depend on GPU. And it produces magnificent results for alignment and for specific interests to deal with difficult dataset. You can't find this flexibility in other software packages now a days as they are mostly automated.

On Wed, 21 Nov, 2018, 22:02 Chan, Lieza (NIH/NIDDK) [F] <[log in to unmask] wrote:

Hello,

 

I am interested in aligning all my particles, and as I have been looking through the Relion documentation, It seems that through the 2D classification step, the particles can be aligned. However, It takes time to create all the 2D classes and I was wondering if there was a less computationally expensive way of aligning the particles  or a way to just parse part of the relion_refine method to only align all the particles without having to create the 2D class averages.

 

Lieza M Chan

 

Postbaccalaureate Research Fellow

National Institute of Diabetes and Digestive and Kidney Diseases 

National Institutes of Health

8 Center Dr, Bethesda MD 20892

 

email: [log in to unmask]

phone: 301.827.3604

 


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