Benchmarking/Comparison

[Mtsaha]

Hi there,

Does anybody know when Auto3DEM should be used and when other packages like EMAN are more suitable?

I mean, how does Auto3DEM compare to other packages like EMAN?

Thanks much,

Mitul

[David Gene Morgan]

Mitul,

autod3em is spectacularly successful with most icosahedral particle
reconstructions. It also has some tools for dealing with icosahedral
particles that are not found in other packages. Other point group
symmetry should be possible using auto3dem, but when I have tried
several of them, I did not have as much luck as I did using EMAN.
auto3dem and EMAN treat CTF correction differently (both at the level of
the algorithmic implimentation and the user input), and I find that the
"setup" for auto3dem is easier than that of EMAN. I'm sure others would
disagree with that assessment.

Having said all that, it really boils down to the choice of which
package you are most familiar with. If you don't know either well, my
suggestion is to try both and decide which works better for your
particular situation.

--
David Gene Morgan
Electron Microscopy Center
047D Simon Hall
IU Bloomington
812 856 1457 (office)
812 856 3221 (3200)
http://bio.indiana.edu/~cryo

[Mtsaha]

Thanks David!

So with icosahedral particles you recommend Auto3dEM?

Best,

Mitul

[Giovanni Cardone]

I would surely recommend to try it.

Giovanni

--

---
You received this message because you are subscribed to the Google Groups "Auto3DEM" group.
To unsubscribe from this group and stop receiving emails from it, send an email to auto3dem+u...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

-- 
Giovanni Cardone
Baker's Laboratory
University of California, San Diego
Department of Chemistry and Biochemistry
9500 Gilman Drive, NSB 4107, MC-0378
La Jolla, CA, 92093-0378
(858)534-5852