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

[Thomas H. <th...@gm...>]

Hi Elizabeth (and everyone),

a new, stable(r) version 0.971 from yesterday is available with the most recent bug fixes.

Please test that by pulling the master branch or downloading the package from sourceforge. 
It will fix most of the more recent problems that were raised through the mailing list.

Cheers
Thomas

> On Feb 17, 2016, at 6:12 PM, Villa, Elizabeth <ev...@uc...> wrote:
> 
> 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
> 
> This program is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
> 
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
> 
> The complete license can be obtained from 
> http://www.gnu.org/licenses/gpl-3.0.html.
> 
> 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
> 
> 
> 
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