[3dem] RCT Reconstruction using EMAN2 and XMIPP

[Carlos Oscar Sorzano]

Dear Kushal,

an easy solution to this is:
1) Convert the coordinates from Eman to Xmipp
2) Open xmipp_micrograph_mark for marking pairs:
        xmipp_micrograph_mark -i untilted.raw -tilted tilted.raw
      Note that Xmipp is expecting the coordinate files to be called:
       untilted.raw.Common.pos
       tilted.raw.Common.pos
      and to be in the same directory as the micrographs.
3) Choose the option "Save angle" in the untilted micrograph. This 
action will recompute the RCT angles.

Kind regards, Carlos Oscar

On 20/07/2011 13:08, 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 
> <mailto:kushal.sejwal at virchow.uni-wuerzburg.de>
> Web: http://virchow.uni-wuerzburg.de/lab_pages/bhushan/
>
>
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-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
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