[3dem] RCT Reconstruction using EMAN2 and XMIPP

[Steven Ludtke]

Hi Kushal. We are developing XMIPP integration for several types of processing for the next major
release of XMIPP, but do not have anything in place to work with current XMIPP versions. You will
probably need to work out the relevant relationship yourself if you want to attempt this. You can
contact John Flanagan Francis <jfflanag at bcm.edu>, the postdoc who wrote e2RCTboxer for info
about the transformations on the EMAN2 side.  As this program is very new, you are unlikely
to find anyone on the 3DEM list who will have experience doing this.

----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Associate Professor, Dept. of Biochemistry and Mol. Biol.      Those who do
Co-Director National Center For Macromolecular Imaging	           ARE
Baylor College of Medicine                                     The converse
sludtke at bcm.edu  -or-  stevel at alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

On Jul 20, 2011, at 4:08 AM, Kushal Sejwal wrote:

> Dear All,
> 
> I want to perform RCT reconstruction on my tilt pair data using both EMAN2 and XMIPP. I am using e2RCTboxer to write .box files, which can easily be converted into XMIPP's .pos file. But XMIPP saves the information about the transformation matrix in the .ang (angle) files. I am unable to find a solution to export/create these .ang files directly from e2RCTboxer. Where is this information saved in EMAN2? How are the angles computed by e2RCTboxer [Computed tilt angle, Computed tilt axis(Y), Gamma angle] correlate with that of XMIPP generated .ang file angles [alpha_u(angle between tilt axis and y-axis of untilted image), alpha_t(angle between tilt axis and y-axis of tilted image), gamma(tilt angle)] ?
> 
> Thanks in anticipation!
> 
> Regards,
> 
> Kushal
> 
> --------------------------------------------------------------------------------
> Kushal Sejwal
> PhD Student, Bhushan Cryo Electron Microscopy Lab
> 
> Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine
> University of Würzburg, Germany
> 
> Phone: +49 931 31 83508
> E-mail: kushal.sejwal at virchow.uni-wuerzburg.de
> Web: http://virchow.uni-wuerzburg.de/lab_pages/bhushan/
> 
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