[Pytom-mail] Fwd: error on the first attempt at tutorial

[Villa, E. <ev...@uc...>]

hi all,  

We’re trying pytom for the first time and we seem to have issues. First we pulled the master branch, and now the devel branch, and we seem to have issues.  Can you please help?  We are following the website/tutorial instructions. 

Cheers, 
Elizabeth 




PyTom v0.97

This license affects the software package PyTom and all the herein distributed source / data files.
Authors: 
Thomas Hrabe
Yuxiang Chen
Friedrich Foerster

Copyright (c) 2008-2016
Max-Planck-Institute for Biochemistry
Dept. Molecular Structural Biology
82152 Martinsried, Germany
http://www.pytom.org

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it under the terms of the GNU General Public License as published by
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sys.version_info(major=2, minor=7, micro=5, releaselevel='final', serial=0)
option --tiltSeriesPath not recognized
RibosFromLysate/reconstructTomo> 




> Begin forwarded message:
> 
> From: Elizabeth Villa <ev...@uc...>
> Subject: Re: error on the first attempt at tutorial
> Date: February 17, 2016 at 5:16:39 PM PST
> To: Thomas Hrabe <th...@sb...>
> Cc: Ittipat Meewan <im...@uc...>
> 
> Hmm.. I just pulled it from the git repository..  Will email the pytom list in the future.. 
> 
> thanks! 
> E
> 
> 
> 
>> On Feb 17, 2016, at 5:06 PM, Thomas Hrabe <th...@sb...> wrote:
>> 
>> Hi E,
>> 
>> haven’t played with the reconstruction before for a while.
>> Seems there’s a unset parameter. Obvious what it does, but do we have a different version running? In my release I find the line in row 178. The file is attached.
>> 
>> Please go through the mailing list next time, that’s the best way to get feedback from either of us, including Yuxiang and the whole pytom community (sometimes :) ).
>> 
>> My file is attached, or you can download the development branch from the GIT repository on sourceforge.
>> 
>> Thomas
>> 
>> 
>> 
>>> On Feb 17, 2016, at 4:23 PM, Villa, Elizabeth <ev...@uc...> wrote:
>>> 
>>> hi T, 
>>> 
>>> We just installed pytom and downloaded the tutorial. In the first attempt at reconstructing the tomo, I get:
>>> 
>>> The complete license can be obtained from 
>>> http://www.gnu.org/licenses/gpl-3.0.html.
>>> 
>>> Tilt Series: ../projections/tomo01_sorted 1-41
>>> Index of Reference Projection21
>>> Marker Filename:../projections/markfile_temp.mark, Index of Reference Marker:1
>>> Handflip:False
>>> Projection Targets: ./alignedProjections/tomo01
>>> FineAlignmentFile: None
>>> Binning Factor of Projections: 4, lowpass filter (in Ny): 0.5
>>> Name of Reconstruction Volume: tomogram.em of Filetype: em
>>> Reconstruction size: ['512', '512', '128']
>>> Reconstruction center: ['0', '0', '0']
>>> Traceback (most recent call last):
>>>   File "/usr/local/pytom/bin/reconstructTomogram.py", line 138, in <module>
>>>     print "write only projections out: "+str(onlyWeightedProjections)
>>> NameError: name 'onlyWeightedProjections' is not defined
>>> [evilla@pordoi reconstructTomo]$ 
>>> 
>>> 
>>> The weird thing is that onlyWeightedProjections  is not a flag in the script, so it must have been a default option that got dropped?  
>>> 
>>> Should we contact Frido’s group about this? 
>>> 
>>> Thanks! 
>>> E
>>> 
>>> 
>>> 
>>> --
>>> Elizabeth Villa
>>> Department of Chemistry and Biochemistry
>>> University of California San Diego 
>>> 
>>> w: villalab.ucsd.edu
>>> v:  +1 (858) 246-1843
>>> f: +1 (858) 534-4864
>>> 
>>> 
>>> 
>> 
>> <reconstructTomogram.py>
> 
> --
> Elizabeth Villa
> Department of Chemistry and Biochemistry
> University of California San Diego 
> 
> w:	villalab.ucsd.edu
> v: 	+1 (858) 246-1843
> f:	+1 (858) 534-4864
> 
> 
> 

--
Elizabeth Villa
Department of Chemistry and Biochemistry
University of California San Diego 

w:	villalab.ucsd.edu
v: 	+1 (858) 246-1843
f:	+1 (858) 534-4864