Re: [Pytom-mail] Tutorial files

[Kanika K. <kk...@uc...>]

Sorry! Thanks for pointing that out. But now it is showing a different
error!

option --filetype Not recognized

On Wed, Feb 24, 2016 at 11:39 AM, Thomas Hrabe <th...@gm...> wrote:

> Hm, I see theres a gap between - and projectionTargets in your call?
>
>
>
> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:
>
> Kanika,
>
> attached is the fixed call for your reconstruction.
>
> The two first parameters had to be replaced
>
> reconstructTomogram.py
> --tiltSeriesName
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted
> --tiltSeriesFormat em
> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
> Works? (Worked for me)
>
> The tutorial will be fixed in a bit.
>
> Thomas
>
> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
>
> Hi,
>
> I used the following command as per the tutorial.
>
> reconstructTomogram.py --tiltSeriesPath
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
> --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
> --referenceIndiex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
>
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>> can you please send the full terminal command and output you processed?
>>
>> Thomas
>>
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hi,
>>
>> I downloaded the tutorial file.
>>
>> I have been trying to use it to reconstruct the tutorial data and I get
>> the following error when I run the script reconstructTomo.
>>
>>
>>
>> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
>> serial=0)option --tiltSeriesPath not recognized*
>>
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>
>
>