[3dem] Re: 3dem Digest, Vol 71, Issue 10
Roberto Marabini
roberto at cnb.csic.es
Mon Jul 15 01:42:33 PDT 2013
Hi,
To make a long history short the mrc files generated by xmipp and
relion are not different. What is different is how the software read
the images.
Follows the long history:
How to differentiate 2D stacks from 3D maps in MRC format was not
being clearly documented until now.
Xmipp policy regarding MRC format was changed in version 3.1 (not
yet released). Prior to version 3.1 file ending in mrc were understood
as volumes and files ending in mrcs were understood as 2D stacks. To
manually force an image file to be read as a volume or stack, write
the filename with the following suffixes, ":mrc" for volume and :mrcs"
for stack.
Starting in version 3.1 we use the following convention: For 3D
maps of single particles ISPG=1 and NSYMBT=0. For 2D image/stack
ISPG=0 and NSYMBT=0. . In case ISPG=401 the data is read as a stack of
volumes, being the mz field in header the number of volumes in the
stack. Finally, MZ=1 for 2D stacks and MZ=NZ for single volumes.
hope this helps
Roberto
On Sun, Jul 14, 2013 at 9:00 PM, <3dem-request at ncmir.ucsd.edu> wrote:
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> Today's Topics:
>
> 1. different mrc formats in relion-1.2 and xmipp-3. ???
> (Dieter Blaas)
> 2. Re: different mrc formats in relion-1.2 and xmipp-3. ???
> (Marin van Heel)
> 3. Re: different mrc formats in relion-1.2 and xmipp-3. ???
> (Dieter Blaas)
> 4. Re: different mrc formats in relion-1.2 and xmipp-3. ???
> (Mike Strauss)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 14 Jul 2013 17:08:05 +0200
> From: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> Subject: [3dem] different mrc formats in relion-1.2 and xmipp-3. ???
> To: 3dem at ncmir.ucsd.edu
> Message-ID: <51E2BED5.9020708 at meduniwien.ac.at>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> 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
>
> --
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories wher
> 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
> ------------------------------------------------------------------------
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 14 Jul 2013 13:40:02 -0300
> From: Marin van Heel <marin.vanheel at googlemail.com>
> Subject: Re: [3dem] different mrc formats in relion-1.2 and xmipp-3.
> ???
> To: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> Cc: 3dem at ncmir.ucsd.edu
> Message-ID: <51E2D462.5030802 at googlemail.com>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
>
>
> 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
>>
>
>
> --
> ================================================================
>
> Marin van Heel
>
>
> Professor of Cryo-EM Data Processing
>
> Leiden University
> Cell Observatory
> NeCEN Building Room 05.27
> Einsteinweg 55
> 2333 CC Leiden
> The Netherlands
>
> Tel. NL: + 31 (0) 715271424
> Mobile NL: + 31 (0) 652736618
> Skype: Marin.van.Heel
>
> and:
>
> Professor of Structural Biology
>
> Imperial College London
> Faculty of Natural Sciences
> Division of Molecular Biosciences
> Biochemistry Building (Room 512)
> South Kensington Campus
> London SW7 2AZ, UK
>
> Tel. UK: + 44 (0) 20 75945316
> Mobile: + 44 (0) 7941540625
>
> email: marin.vanheel(A_T)gmail.com
> email: m.vanheel(A_T)ic.ac.uk
> and: mvh.office(A_T)gmail.com
>
>
> I receive many emails per day and, although I try, there is no guarantee that I will actually read each incoming email. Moreover, our Spam filters can be strikt and sometimes make legitimate emails disappear (try the gmail accounts, alternatively)
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 14 Jul 2013 19:53:34 +0200
> From: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> Subject: Re: [3dem] different mrc formats in relion-1.2 and xmipp-3.
> ???
> To: 3dem at ncmir.ucsd.edu
> Message-ID: <51E2E59E.2030503 at meduniwien.ac.at>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> 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
>>>
>>
>>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 14 Jul 2013 14:03:54 -0400
> From: Mike Strauss <mikestrauss13 at crystal.harvard.edu>
> Subject: Re: [3dem] different mrc formats in relion-1.2 and xmipp-3.
> ???
> To: Dieter Blaas <dieter.blaas at meduniwien.ac.at>
> Cc: 3dem at ncmir.ucsd.edu
> Message-ID: <6BB772E3-4682-4952-9034-7943E822D274 at crystal.harvard.edu>
> Content-Type: text/plain; charset=us-ascii
>
> 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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>
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>
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