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Re: [Pytom-mail] Particle information extraction
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From: Thomas H. <th...@gm...> - 2016-09-13 18:03:04
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Hi Kanika,
EM is currently still the format PyTom was tested on exhaustively. MRC is supported, but there are be some issue still as you see.
If the conversion works for you, I suggest to keep it up for your project and not change your protocols for such minor issues.
However, I agree that MRC support should be improved in the future.
Cheers,
Thomas
> On Sep 8, 2016, at 1:48 PM, Kanika Khanna <kk...@uc...> wrote:
>
> 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... <mailto: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... <mailto: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!
>> ------------------------------------------------------------------------------
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>
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