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

[Sjors Scheres]

Hi Dieter,

I agree completely with Marin. The MRC format does not do 4D data, so I
have no clue on what Xmipp bases this different behaviour regarding
Nr_objects or Z_dim. This seems a question for the Xmipp developers. I am
CC-ing Roberto Marabini.

Best wishes,
Sjors


> 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.
>
> Cheers
>
> Marin
>
>
> 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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>
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>
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>
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>
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-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres