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

Marin van Heel marin.vanheel at googlemail.com
Sun Jul 14 13:41:53 PDT 2013

Dear Dieter

I understand you only have one 3D data set.  The problem however is that 
apparently these programs handle your one 3D data set with two different 
definitions of a 4D data set. In both cases one of the 4 dimensions is 
set to unity (after all there is only one 3D volume). The programs 
apparently use a different position for the (N)Objects variable which in 
both cases is set to "1".  Since the MRC/CCP4 format does not 
support/define this fourth dimension these two different 4D formats are 
both (mulually incompatible) extensions to the MRC/CCP4 format .

Hope I have been clearer this time around.



On 14-Jul-13 2:53 PM, Dieter Blaas wrote:
> 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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     Marin van Heel

     Professor of Cryo-EM Data Processing

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