Re: [Pytom-mail] Pytom-mail post from khannakanika11@gmail.com requires approval

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

Hello Thomas

1. I have submitted the job for localization using command line and haven't
really gotten any result files (scores.em/angles.em)

This is the command I entered as per the tutorial:

 localizationJob.py -v tomogram.mrc -r emdb.mrc -m mask.em --wedge1 30
--wedge2 30 -a angles_12.85_7112.em -d /home/kkhanna/Documents/Pytom/ -b 0
--splitX 2 --splitY 2 -j job.xml

Do you want me to send the tomogram/reference file etc.?
When I had run the command, there wasn't any error either.

2. Also, in the previous mail, you sent the .em files for PDBs. Thanks for
that. I notice that the files with individual chains 3uzoA.em and 3uzoB.em
are in cubes and the full file 3uzofull.em is density map. When I try to
generate the EM files with pdb2em, the option to enter the cube size is a
strict yes. How is it then possible to generate the files with EM map and
which files are supposed to be used for localization in that case?

Thanks!





On Thu, Feb 18, 2016 at 3:19 PM, Thomas Hrabe <th...@gm...> wrote:

> Hi Kanika,
>
> the link to the chimera plugin with installation tutorial is back up:
>
> http://www.biochem.mpg.de/309018/PyTom
>
> Best,
> Thomas
>
> On Feb 18, 2016, at 1:47 PM, Thomas Hrabe <th...@gm...> wrote:
>
> Hi Kanika,
>
> Thank you for your interest in pytom.
>
> 1. It seems that the atomList is empty -> devision by zero from what I can
> tell from your error. By the way, are you sure you have old style PDB files
> or the new mmCIF file format (the new ones are not compatible yet, or at
> least in development are)
>
> 2. the scores and angles should be in the result folder you specify.
>
> I just checked the Chimera plugin page on the Foerster group page.
> We will update the links soon.
>
> Thanks,
> Thomas
>
>
>
>
>
>
>
> On Feb 18, 2016, at 1:32 PM, pyt...@li... wrote:
>
> As list administrator, your authorization is requested for the
> following mailing list posting:
>
>    List:    Pyt...@li...
>    From:    kha...@gm...
>    Subject: Particle extraction and pdb2em
>    Reason:  Post by non-member to a members-only list
>
> At your convenience, visit:
>
>    https://lists.sourceforge.net/lists/admindb/pytom-mail
>
> to approve or deny the request.
>
> *From: *Kanika Khanna <kha...@gm...>
> *Subject: **Particle extraction and pdb2em*
> *Date: *February 18, 2016 at 1:31:48 PM PST
> *To: *pyt...@li...
>
>
> Hello,
>
> I am new to pytom and have the following questions:
>
> 1. pdb2em: I type in the following to convert my pdb file to em file:
>
> pdb2em.py -p "pathtopdbfile" -s 4 -v 50 -o "pathtoemfile" and get the
> following error message:
> Traceback (most recent call last):
>   File "/usr/local/pytom/bin/pdb2em.py", line 41, in <module>
>     volume = pdb2em(pdbFile, float(pixelSize), int(cubeSize), chain =
> chain,densityNegative = densityNegative)
>   File "/usr/local/pytom/basic/files.py", line 369, in pdb2em
>     return atomList2em(atomList,pixelSize,cubeSize,densityNegative)
>   File "/usr/local/pytom/basic/files.py", line 297, in atomList2em
>     centroidX = centroidX / len(atomList)
> ZeroDivisionError: integer division or modulo by zero
>
>
> Any ideas as to what might be wrong?
>
> 2. Once we have the localization file created as .xml and .sh file, how do
> we get the scores.em and angles.em file for particle extraction? How to
> visualize these files in chimera using the plugin mentioned in your website
> (volumedialog_new.py)?
>
> Thanks!
>
> --
> Best
> Kanika Khanna
> Graduate Student, Biological Sciences Department
> University of California, San Diego
>
>
>
> *From: *pyt...@li...
> *Subject: **confirm 6616e7ea858ae6f8d6a87e73a557d843a511c7d5*
>
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