Hi,
> gotten round to using relion3.1. But could you explain what the
> _rlnImageDimensionality field is? You mentioned that for SPA one
> should enter 2, does it mean XY dims?
Yes.
> Does this then also mean that
> 3.1 one could potentially take 3D coords for subtomogram averaging?
For 3D subtomogram averaging, each "particle" is a small 3D volume,
so the dimensionality is 3. I myself have never used this functionality
and I cannot provide support for it.
Best regards,
Takanori Nakane
> Best,
> Pranav
> --
> Pranav Shah
> Postdoctoral Research Fellow.
>
> Division of Structural Biology,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford,
> Roosevelt Drive, Oxford OX3 7BN,
> UK
>
> On Mon, Dec 30, 2019 at 11:40 PM Takanori Nakane
> <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> Does csparc2star.py output in RELION 3.0 format, or 3.1 format?
>>
>> If it is 3.0 format, make sure particle images are available
>> before importing the file or running relion_convert_star.
>> Otherwise, 3.0-to-3.1 conversion cannot fill the box size and the
>> dimensionality fields.
>>
>> If it is 3.1 format, make sure the optics table in the
>> STAR file contains "_rlnImageSize" item (box size in pixels)
>> and "_rlnImageDimensionality" (should be 2 for SPA).
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2019/12/30 23:34, eswar reddy wrote:
>>> Dear all,
>>> I keep getting error in relion 3.1; when I tried to run a 3D
>>> classification job using the particles that have been extracted and 2D
>>> classified in cryosparc, I have used csparc2star.py command to convert
>>> cs file to star file. I have supplemented the generated star file and a
>>> reference map that I have obtained from Ab-initio classification of
>>> cryosparc to do a 3D job in relion
>>> *
>>> *
>>> *WARNING: input particles STAR file does not have a column for image
>>> dimensionality, assuming 2D images ...
>>> in: /home/software/cryoem/relion/src/jaz/obs_model.cpp, line 688
>>> ERROR:
>>> ObservationModel::getBoxSize: box sizes not available. Make sure
>>> particle images are available before converting/importing STAR files
>>> from earlier versions of RELION.
>>>
>>> === Backtrace ===
>>> /usr/local/relion/bin/relion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41)
>>> [0x434671]
>>> /usr/local/relion/bin/relion_refine(_ZNK16ObservationModel10getBoxSizeEi+0x6b)
>>> [0x4fcd0b]
>>> /usr/local/relion/bin/relion_refine(_ZN7MlModel20initialiseFromImagesE8FileNamebR10ExperimentRbS3_S3_dbb+0xc9)
>>> [0x60c499]
>>> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x4ff)
>>> [0x4827ef]
>>> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x2f)
>>> [0x48522f]
>>> /usr/local/relion/bin/relion_refine(main+0x33) [0x427bc3]
>>> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f6828084505]
>>> /usr/local/relion/bin/relion_refine() [0x42865f]
>>> ==================
>>> ERROR:
>>> ObservationModel::getBoxSize: box sizes not available. Make sure
>>> particle images are available before converting/importing STAR files
>>> from earlier versions of RELION.*
>>> *
>>> *
>>> What might went wrong,**
>>> *Best regards, *
>>> *E.R*
>>>
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