Re: [Pytom-mail] Particle information extraction

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

Thank you!

I had another quick question. When I am trying to run localization jobs, I
am only able to run if I convert my .rec files (which are essentially mrc
format) to em format using mrc2em.py . If I try to run the localization
with .rec or .mrc format, I get the following error:
Traceback (most recent call last):

  File "/usr/local/pytom/bin/localization.py", line 82, in <module>
    startLocalizationJob(jobName, splitX, splitY, splitZ,
doSplitAngles=False)
  File "/usr/local/pytom/bin/localization.py", line 21, in
startLocalizationJob
    leader.parallelRun(job, splitX, splitY, splitZ, verbose)
  File "/usr/local/pytom/localization/parallel_extract_peaks.py", line
1046, in parallelRun
    result = self.run(verbose)
  File "/usr/local/pytom/localization/parallel_extract_peaks.py", line 83,
in run
    v = self.volume.getVolume(self.volume.subregion)
  File "/usr/local/pytom/localization/structures.py", line 55, in getVolume
    binning[0], binning[1], binning[2])
  File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 378, in
read
    return _pytom_volume.read(*args)
RuntimeError: Reading CCP4 file: the datatype in the file is not supported!

For information, both my pdb and mask are in em format as well.


On Wed, Sep 7, 2016 at 12:06 PM, Thomas Hrabe <th...@gm...> wrote:

> Hi Kanika,
>
> Code between the lines. When you try to access information from a
> ParticleList, you must read it first from disk. You were trying to read the
> wrong type - PickPosition - instead of ParticleList
>
> Replace PickPosition with ParticleList
>
> Hope it helps solving your problem,
> Thomas
>
> On Sep 7, 2016, at 12:00 PM, Kanika Khanna <kk...@uc...> wrote:
>
> Hello all,
>
> I have been trying to get coordinates of X,Y,Z from particle list using
> the function 'PickPosition' from ipytom as follows:
> ipytom
> from pytom.basic.structures import PickPosition
>
>
> from pytom.basic.structures import ParticleList
>
> pl=PickPosition()
> pl.fromXMLFile(pl.xml’)
>
>
> for i,p in enumerate(pl):
> p.getPickPosition()
>
> or
> pl[i].getPickPosition()
>
>
>
>
> But I run into the following error:
> UnboundLocalError                         Traceback (most recent call last)
> <ipython-input-5-71b11edb47f3> in <module>()
> ----> 1 pl.fromXMLFile ('pl.xml')
>
> /usr/local/pytom/basic/structures.py in fromXMLFile(self, filename)
>      72         lines = readStringFile(filename)
>      73
> ---> 74         self.fromStr(lines)
>      75
>      76     def toXMLFile(self,filename):
>
> /usr/local/pytom/basic/structures.py in fromStr(self, string)
>      45         root = etree.fromstring(string)
>      46
> ---> 47         self.fromXML(root)
>      48
>      49     def __str__(self):
>
> /usr/local/pytom/basic/structures.py in fromXML(self, xmlObj)
>    3674             TypeError('PickPosition: You must provide a valid
> PickPosition XML object.')
>    3675
> -> 3676         self._x = float(shift_element.get('X'))
>    3677         self._y = float(shift_element.get('Y'))
>    3678         self._z = float(shift_element.get('Z'))
>
> UnboundLocalError: local variable 'shift_element' referenced before
> assignment
>
>
> Am I doing it right? How can I get the X,Y,Z coordinates of particles in a
> matrix from particle file?
>
> Thanks!
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Pytom-mail mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytom-mail
>
>
>