[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
paper:
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.
Cheers,
Marin
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
Leiden University
Cell Observatory
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2333 CC Leiden
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Skype: Marin.van.Heel
and:
Professor of Structural Biology
Imperial College London
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