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

[Mike Strauss]

You can change the header using imedit.exe from the mrc package (image2010).  Or you may be able to use alterheader from the IMOD package.

regards,

mike

On Jul 14, 2013, at 1:53 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> 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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