[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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