[3dem] different mrc formats in relion-1.2 and xmipp-3. ???

Marin van Heel marin.vanheel at googlemail.com
Sun Jul 14 09:40:02 PDT 2013

Dear Dieter,

Unfortunately, the MRC/CCP4 format does not support 4D data sets! Since 
there is no standard defined, "anything goes" in terms of extending that 
specific format. The best you can do in terms of the MRC/CCP4 format is 
to create a set of different 3D volume files and handle them separately 
one by one.

Have a look at what we have written about 4D formats in the IMAGIC 4D 

Van Heel M, Portugal R, Rohou A, Linnemayr C, Bebeacua C, Schmidt R, 
Grant TR & Schatz M. Four-Dimensional Cryo Electron Microscopy at Quasi 
Atomic Resolution: IMAGIC 4D. International Tables for Crystallography 
Volume F: Crystallography of biological macromolecules (Second Edition) 
Editors: E. Arnold, D. M. Himmel and M. G. Rossmann. International 
Tables for Crystallography Vol. F (2012) 624-628.



On 14-Jul-13 12:08 PM, Dieter Blaas wrote:
> Hi,
>      I noticed that (at least) some (or all?) of the routines of 
> relion and xmipp output different mrc-formats as revealed with 
> "xmipp_image_header".  For example, a file created with xmipp (e.g. a 
> with "xmipp_phantom_create")  has "Dimensions     : 1 x 244 x 244 x 
> 244  ((N)Objects x (Z)Slices x (Y)Rows x (X)Columns)" whereas files 
> created with relion have  "Dimensions     : 244 x 1 x 244 x 244  
> ((N)Objects x (Z)Slices x (Y)Rows x (X)Columns)". When trying to work 
> on a file like the latter with xmipp I get an error message (e.g in 
> "in xmipp_transform_symmetrize" like
>  " _ERROR 3:  Argument missing
> The symmetry order is not valid for images
> File: libraries/reconstruction/symmetrize.cpp line: 161"
> What is wrong? Is there a way of easily fix this?
>  Thanks for hints, Dieter


     Marin van Heel

     Professor of Cryo-EM Data Processing

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