Supervised classification


Outline


Recent modifications


Getting started

  1. Download and unpackage a tarball from the archive. The files will be extracted to the current directory. (The alternative would be to create a new directory, but people may run classifications more than once on the same data set, and I didn't want to risk overwriting files.)
  2. You will need the following inputs (change labels in batch file if necessary)

Batch files


More than two references

The above batch files are helpful for discerning between two references, but when there are more than two references, it would be impractical to try all combinations of pairs of references in order to calculate the deltaCC. Instead, I wrote the following batch file:


Parallel usage

I have an experimental set of batch files based on realign-orsh.spi that I recently started to use. Specifically, it tries to prevent all nodes trying to read the image-stacks at the same time by giving the previous defocus group a head-start. By default, I have this parameter set to 600 seconds (10 minutes). The flow is as follows:


References

  1. Valle M, Sengupta J, Swami NK, Grassucci RA, Burkhardt N, Nierhaus KH, Agrawal RK, Frank J. (2002) Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21: 3557-67.
  2. Gao H, Valle M, Ehrenberg M, Frank J. (2004) Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J Struct Biol. 147: 283-90
  3. Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc. 3: 1941-74.

Source: techs/supclass/supclass.htm     Page updated: 2012/12/11     Tapu Shaikh