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

Dieter Blaas dieter.blaas at meduniwien.ac.at
Sun Jul 14 10:53:34 PDT 2013

Dear Marin,
    thanks for the hint, but isn't that a misunderstanding?

I am not talking about a set of 3D volumes but just one 3D volume that 
seems to be defined differently when output from xmipp-3.0 and 
relion-1.2. Is there a way of changing the data in the header from  244 
x 1 x 244 x 244 to 1 x 244 x 244 x 244? If so, everything might be fine!

best, Dieter

Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: dieter.blaas at meduniwien.ac.at

Am 14.07.2013 18:40, schrieb Marin van Heel:
> 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

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