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Re: [scipion-users] Error during particle extraction after Localized reconstruction job
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From: Karim R. <kar...@um...> - 2019-11-12 17:00:47
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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...<mailto: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.png] Hope that helps, Best, Jose Miguel On Tue, Nov 12, 2019 at 3:09 PM Karim Rafie <kar...@um...<mailto: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...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
