Re: [scipion-users] Error during particle extraction after Localized reconstruction job

[Jose M. de la R. T. <del...@gm...>]

No problem.

Thanks for letting me know.

On Tue, Nov 12, 2019, 6:01 PM Karim Rafie <kar...@um...> wrote:

> Hi Jose and all,
>
>
> I found it after searching a bit more. Sorry for the spam.
>
>
> Best wishes,
>
> Karim
>
> ##############################################
>
> Karim Rafie; PhD, AMRSC
>
> Postdoctoral Research Fellow
>
> Carlson Lab
>
> Department of Medical Biochemistry and Biophysics
>
> Umeå University
>
> Umeå / Sweden
> ------------------------------
> *From:* Karim Rafie <kar...@um...>
> *Sent:* 12 November 2019 17:02:50
> *To:* Mailing list for Scipion users
> *Subject:* Re: [scipion-users] Error during particle extraction after
> Localized reconstruction job
>
> Hi Jose,
>
> Thanks a lot for the help. It does make sense. I did look for the
> localised extraction protocol but couldn't find it. Is there a particular
> plug in that I need to have for it? When choosing the localised
> reconstruction tool set from the drop down menu I only get the compute sub
> particle job.
>
> Best,
> Karim
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
>
>
>
> On Tue, Nov 12, 2019 at 3:17 PM +0100, "Jose Miguel de la Rosa Trevin" <
> del...@gm...> wrote:
>
> Dear Karim,
>>
>> The computed sub-particles are kind of particles, but not exactly, since
>> they come from other particles, not micrographs.
>> That's is the error here..expecting micrograph in these protocols you
>> tried. Still, I understand that might be confusing
>> and we should put some validation to prevent it.
>>
>> You should use instead of the localrec - localized extraction protocol as
>> shown below:
>>
>> [image: image.png]
>>
>> Hope that helps,
>> Best,
>> Jose Miguel
>>
>>
>>
>> On Tue, Nov 12, 2019 at 3:09 PM Karim Rafie <kar...@um...> wrote:
>>
>>> Dear all,
>>>
>>>
>>> I'm trying to perform a localized reconstruction on a sub-particle of my
>>> structure. I used the "compute sub-particles" job in scipion-v2.0 to
>>> generate the coordinates of the sub-particles, however when I want to
>>> extract them with relion-extract I get the following error message:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *"   Traceback (most recent call last): 00011:     File
>>> "/usr/local/bin/scipion/pyworkflow/protocol/protocol.py", line 186, in run
>>> 00012:       self._run() 00013:     File
>>> "/usr/local/bin/scipion/pyworkflow/protocol/protocol.py", line 1283, in
>>> _run 00014:       self._insertAllSteps()  # Define steps for execute later
>>> 00015:     File
>>> "/usr/local/bin/scipion/pyworkflow/em/protocol/protocol_particles.py", line
>>> 171, in _insertAllSteps 00016:       micDict = self._loadInputList()
>>> 00017:     File
>>> "/usr/local/bin/scipion/pyworkflow/em/protocol/protocol_particles.py", line
>>> 359, in _loadInputList 00018:       micDict, self.micsClosed =
>>> _loadMics(coordMics) 00019:     File
>>> "/usr/local/bin/scipion/pyworkflow/em/protocol/protocol_particles.py", line
>>> 350, in _loadMics 00020:       lambda mic: mic.getMicName()) 00021:
>>> File "/usr/local/bin/scipion/pyworkflow/em/protocol/protocol_particles.py",
>>> line 340, in _loadSet 00022:       micKey = getKeyFunc(item) 00023:
>>> File "/usr/local/bin/scipion/pyworkflow/em/protocol/protocol_particles.py",
>>> line 350, in <lambda> 00024:       lambda mic: mic.getMicName()) 00025:
>>> AttributeError: 'Particle' object has no attribute 'getMicName' 00026:
>>> ------------------- PROTOCOL FAILED (DONE 0/0)"*
>>>
>>>
>>> I get the same error, when wanting to extract the particles with xmipp.
>>> Is this a bug or am I doing something wrong?
>>>
>>>
>>> Any help would be greatly appreciated.
>>>
>>>
>>> Best wishes,
>>>
>>> Karim
>>>
>>> ##############################################
>>>
>>> Karim Rafie; PhD, AMRSC
>>>
>>> Postdoctoral Research Fellow
>>>
>>> Carlson Lab
>>>
>>> Department of Medical Biochemistry and Biophysics
>>>
>>> Umeå University
>>>
>>> Umeå / Sweden
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
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