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From: Grigory S. <sha...@gm...> - 2022-07-12 15:37:26
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Dear Hong, There's no test with such a name. You can get the list of tests by running: scipion3 test --grep relion Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Tue, Jul 12, 2022 at 4:30 PM HONG ZHAN via scipion-users < sci...@li...> wrote: > Dear Scipion group, > > My name is Hong Zhan and research scientist at the University of > Wisconsin-Madison. I am recently trying out Scipion-tomo package on my > CryoET project. I am very interested in the workflow and particularly am > interested in pyseg. > > Os: Ubuntu 20.0.4; scipion-em updated version. > > I installed the scipion3 and along with plugins. However, it seems my > relion related tests failed. But Cistem and others are fine. Would be great > to have some help on the issues. I have relion3 and relion4 enabled. But it > seems not find the relion test file, would be name changed? > Super thanks! > Hong > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: HONG Z. <hz...@wi...> - 2022-07-12 15:29:43
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Dear Scipion group, My name is Hong Zhan and research scientist at the University of Wisconsin-Madison. I am recently trying out Scipion-tomo package on my CryoET project. I am very interested in the workflow and particularly am interested in pyseg. Os: Ubuntu 20.0.4; scipion-em updated version. I installed the scipion3 and along with plugins. However, it seems my relion related tests failed. But Cistem and others are fine. Would be great to have some help on the issues. I have relion3 and relion4 enabled. But it seems not find the relion test file, would be name changed? Super thanks! Hong |
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From: Lugmayr, W. <w.l...@uk...> - 2022-06-23 14:52:57
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Dear developers,
I updated all scipion plugins today incl. xmipptomo (from git devel):
When I try to go over the tutorial "Subtomo Averaging Ribosome" I get the following error in the step above:
00001: Traceback (most recent call last):
00002: File "/beegfs/cssb/software/em/scipion/3.0/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
00003: self._run()
00004: File "/beegfs/cssb/software/em/scipion/3.0/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
00005: resultFiles = self._runFunc()
00006: File "/beegfs/cssb/software/em/scipion/3.0/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
00007: return self._func(*self._args)
00008: File "/beegfs/cssb/software/em/scipion/3.0/miniconda/envs/scipion3/lib/python3.8/site-packages/xmipptomo/protocols/protocol_project_top.py", line 129, in createOutputStep
00009: coord.setX(subtomo.getCoordinate3D().getX(const.BOTTOM_LEFT_CORNER))
00010: File "/beegfs/cssb/software/em/scipion/3.0/devel/scipion-em-tomo/tomo/objects.py", line 1002, in getX
00011: return self._x.get() - self._getOffset(0, originFunction)
00012: File "/beegfs/cssb/software/em/scipion/3.0/devel/scipion-em-tomo/tomo/objects.py", line 994, in _getOffset
00013: origin_Scipion = self.getVolumeOrigin()[dim]
00014: File "/beegfs/cssb/software/em/scipion/3.0/devel/scipion-em-tomo/tomo/objects.py", line 1197, in getVolumeOrigin
00015: raise Exception("3D coordinate must be referred to a volume to get its origin.")
00016: Exception: 3D coordinate must be referred to a volume to get its origin.
00017: Protocol failed: 3D coordinate must be referred to a volume to get its origin.
and:
00005: PID: 28105
00006: pyworkflow: 3.0.20
00007: plugin: xmipptomo
00008: plugin v: 3.0.8
00009: currentDir: /xxxxxxxx/Scipion3_Tomo_STA_Ribosome
00010: workingDir: Runs/000289_XmippProtSubtomoProject
00011: runMode: Restart
00012: MPI: 1
00013: threads: 1
00014: Starting at step: 1
00015: Running steps
00016: STARTED: projectZStep, step 1, time 2022-06-23 16:24:56.524428
00017: FINISHED: projectZStep, step 1, time 2022-06-23 16:25:06.754856
00018: STARTED: createOutputStep, step 2, time 2022-06-23 16:25:06.903145
00019: Protocol failed: 3D coordinate must be referred to a volume to get its origin.
00020: FAILED: createOutputStep, step 2, time 2022-06-23 16:25:06.970330
00021: *** Last status is failed
00022: ------------------- PROTOCOL FAILED (DONE 2/2)
Cheers,
Wolfgang
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From: C.J. <bi...@gm...> - 2022-06-09 23:36:55
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Thanks! After update xmipp, it works now. Pablo Conesa <pc...@cn...> 于2022年6月9日周四 06:50写道： > You need to update the core: > > These messages you are getting: > > The package scipion-pyworkflow is out of date. Your version is 3.0.18, the > latest is 3.0.20. > The package scipion-em is out of date. Your version is 3.0.13, the latest > is 3.0.17. > The package scipion-app is out of date. Your version is 3.0.9, the latest > is 3.0.10. > Means there is new code that is recomended to update. > > It can be done with: > > "scipion3 update" > > On 9/6/22 0:20, C.J. wrote: > > Hi, > > I followed the guide ( > https://github.com/I2PC/xmipp#standalone-installation) and install xmipp > and link to scipion in scipion.conf. > But there is some issue when launch scipion. > $ scipion > Scipion v3.0.9 - Eugenius > The package scipion-pyworkflow is out of date. Your version is 3.0.18, the > latest is 3.0.20. > The package scipion-em is out of date. Your version is 3.0.13, the latest > is 3.0.17. > The package scipion-app is out of date. Your version is 3.0.9, the latest > is 3.0.10. > > error when importing from xmipp3.protocols: cannot import name > 'setMRCSamplingRate' from 'pwem.convert.headers' > (/data2/sw/scipion3/scipion-em/pwem/convert/headers.py) > File > "/data2/sw/xmipp/xmipp-bundle/src/scipion-em-xmipp/xmipp3/protocols/protocol_rotate_volume.py", > line 30, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager > window) > or use 'scipion installp --help --checkUpdates' in the command line to > check for upgrades, > it could be a versions compatibility issue. > > There is still no xmipp in scipion GUI. Do I still miss anything? > > Thanks! > Jianhao > > > Alberto Garcia Mena <alb...@cn...> 于2022年6月6日周一 01:20写道： > >> Hi again, >> >> To install xmipp devel please follow this guide: >> https://github.com/I2PC/xmipp#standalone-installation >> On 4/6/22 1:08, C.J. wrote: >> >> Hi, I try to install xmipp but there is a question in the output log (see >> attached picture). How can I response to the question? I can't click it or >> type in the log. It's only a text display in the output log. >> >> Thanks! >> Jianhao >> >> <jam...@gm...> 于2022年5月27日周五 15:23写道： >> >>> I think you need xmipp. emlib can point to that. >>> >>> Best wishes >>> James >>> >>> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >>> >>> >>> Hi, >>> >>> I have some issue (see the attached picture) while exporting particles. >>> Did I miss something when installing SCIPION? >>> >>> Thanks! >>> Jianhao >>> >>> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >>> >>>> Hi Jianhao, >>>> >>>> As Grigory pointed out, you can indeed run 'relion - export particles' >>>> on the output of 'localrec - extract subparticles' to accomplish what you >>>> want. >>>> >>>> Cheers, >>>> Serban >>>> ------------------------------ >>>> *From:* C.J. <bi...@gm...> >>>> *Sent:* 27 May 2022 13:18 >>>> *To:* Mailing list for Scipion users < >>>> sci...@li...> >>>> *Subject:* Re: [scipion-users] export particles and metadata >>>> >>>> Hi, these particles are re-extracted by localrec. Soooo, i don't think >>>> relion can do that. >>>> >>>> Jianhao >>>> >>>> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： >>>> >>>> Hi, >>>> >>>> I don't know about localrec plugin but relion plugin has an export >>>> particle protocol that does exactly that. >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: >>>> >>>> Hi, >>>> >>>> I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I >>>> export both particles and metadata into relion3 star file and particles? >>>> >>>> Thank you! >>>> Jianhao >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> [image: Untitled.png]_______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> -- >> - Alberto GM - >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2022-06-09 13:50:10
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You need to update the core: These messages you are getting: The package scipion-pyworkflow is out of date. Your version is 3.0.18, the latest is 3.0.20. The package scipion-em is out of date. Your version is 3.0.13, the latest is 3.0.17. The package scipion-app is out of date. Your version is 3.0.9, the latest is 3.0.10. Means there is new code that is recomended to update. It can be done with: "scipion3 update" On 9/6/22 0:20, C.J. wrote: > Hi, > > I followed the guide > (https://github.com/I2PC/xmipp#standalone-installation) and install > xmipp and link to scipion in |scipion.conf. > | > But there is some issue when launch scipion. > $ scipion > Scipion v3.0.9 - Eugenius > The package scipion-pyworkflow is out of date. Your version is 3.0.18, > the latest is 3.0.20. > The package scipion-em is out of date. Your version is 3.0.13, the > latest is 3.0.17. > The package scipion-app is out of date. Your version is 3.0.9, the > latest is 3.0.10. > > error when importing from xmipp3.protocols: cannot import name > 'setMRCSamplingRate' from 'pwem.convert.headers' > (/data2/sw/scipion3/scipion-em/pwem/convert/headers.py) > File > "/data2/sw/xmipp/xmipp-bundle/src/scipion-em-xmipp/xmipp3/protocols/protocol_rotate_volume.py", > line 30, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager > window) > or use 'scipion installp --help --checkUpdates' in the command line > to check for upgrades, > it could be a versions compatibility issue. > > There is still no xmipp in scipion GUI. Do I still miss anything? > > Thanks! > Jianhao > > > Alberto Garcia Mena <alb...@cn...> 于2022年6月6日周一 > 01:20写道： > > Hi again, > > To install xmipp devel please follow this guide: > https://github.com/I2PC/xmipp#standalone-installation > > On 4/6/22 1:08, C.J. wrote: >> Hi, I try to install xmipp but there is a question in the output >> log (see attached picture). How can I response to the question? I >> can't click it or type in the log. It's only a text display in >> the output log. >> >> Thanks! >> Jianhao >> >> <jam...@gm...> 于2022年5月27日周五 15:23写道： >> >> I think you need xmipp. emlib can point to that. >> >> Best wishes >> James >> >>> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >>> >>> >>> Hi, >>> >>> I have some issue (see the attached picture) while exporting >>> particles. Did I miss something when installing SCIPION? >>> >>> Thanks! >>> Jianhao >>> >>> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >>> >>> Hi Jianhao, >>> >>> As Grigory pointed out, you can indeed run 'relion - >>> export particles' on the output of 'localrec - extract >>> subparticles' to accomplish what you want. >>> >>> Cheers, >>> Serban >>> ------------------------------------------------------------------------ >>> *From:* C.J. <bi...@gm...> >>> *Sent:* 27 May 2022 13:18 >>> *To:* Mailing list for Scipion users >>> <sci...@li...> >>> *Subject:* Re: [scipion-users] export particles and >>> metadata >>> Hi, these particles are re-extracted by localrec. Soooo, >>> i don't think relion can do that. >>> >>> Jianhao >>> >>> Grigory Sharov <sha...@gm...> >>> 于2022年5月27日周五 02:26写道： >>> >>> Hi, >>> >>> I don't know about localrec plugin but relion plugin >>> has an export particle protocol that does exactly that. >>> >>> Best regards, >>> Grigory >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Fri, May 27, 2022 at 12:32 AM C.J. >>> <bi...@gm...> wrote: >>> >>> Hi, >>> >>> I run localrec in SCIPION v3.0.9 to extract >>> subparticles. But how can I export both >>> particles and metadata into relion3 star file >>> and particles? >>> >>> Thank you! >>> Jianhao >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> Untitled.png_______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Alberto G. M. <alb...@cn...> - 2022-06-09 05:43:23
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Hi again Jianhao, Once you donwload and compile Xmipp, you have to link it to scipion <https://github.com/I2PC/xmipp#linking-standalone-version-to-scipion> with /./scipion3 installp -p (pathOfXmippDevel/src/scipion-em-xmiipp --devel/ Tell me if following this step it works Thanks On 9/6/22 0:20, C.J. wrote: > Hi, > > I followed the guide > (https://github.com/I2PC/xmipp#standalone-installation) and install > xmipp and link to scipion in |scipion.conf. > | > But there is some issue when launch scipion. > $ scipion > Scipion v3.0.9 - Eugenius > The package scipion-pyworkflow is out of date. Your version is 3.0.18, > the latest is 3.0.20. > The package scipion-em is out of date. Your version is 3.0.13, the > latest is 3.0.17. > The package scipion-app is out of date. Your version is 3.0.9, the > latest is 3.0.10. > > error when importing from xmipp3.protocols: cannot import name > 'setMRCSamplingRate' from 'pwem.convert.headers' > (/data2/sw/scipion3/scipion-em/pwem/convert/headers.py) > File > "/data2/sw/xmipp/xmipp-bundle/src/scipion-em-xmipp/xmipp3/protocols/protocol_rotate_volume.py", > line 30, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager > window) > or use 'scipion installp --help --checkUpdates' in the command line > to check for upgrades, > it could be a versions compatibility issue. > > There is still no xmipp in scipion GUI. Do I still miss anything? > > Thanks! > Jianhao > > > Alberto Garcia Mena <alb...@cn...> 于2022年6月6日周一 > 01:20写道： > > Hi again, > > To install xmipp devel please follow this guide: > https://github.com/I2PC/xmipp#standalone-installation > > On 4/6/22 1:08, C.J. wrote: >> Hi, I try to install xmipp but there is a question in the output >> log (see attached picture). How can I response to the question? I >> can't click it or type in the log. It's only a text display in >> the output log. >> >> Thanks! >> Jianhao >> >> <jam...@gm...> 于2022年5月27日周五 15:23写道： >> >> I think you need xmipp. emlib can point to that. >> >> Best wishes >> James >> >>> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >>> >>> >>> Hi, >>> >>> I have some issue (see the attached picture) while exporting >>> particles. Did I miss something when installing SCIPION? >>> >>> Thanks! >>> Jianhao >>> >>> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >>> >>> Hi Jianhao, >>> >>> As Grigory pointed out, you can indeed run 'relion - >>> export particles' on the output of 'localrec - extract >>> subparticles' to accomplish what you want. >>> >>> Cheers, >>> Serban >>> ------------------------------------------------------------------------ >>> *From:* C.J. <bi...@gm...> >>> *Sent:* 27 May 2022 13:18 >>> *To:* Mailing list for Scipion users >>> <sci...@li...> >>> *Subject:* Re: [scipion-users] export particles and >>> metadata >>> Hi, these particles are re-extracted by localrec. Soooo, >>> i don't think relion can do that. >>> >>> Jianhao >>> >>> Grigory Sharov <sha...@gm...> >>> 于2022年5月27日周五 02:26写道： >>> >>> Hi, >>> >>> I don't know about localrec plugin but relion plugin >>> has an export particle protocol that does exactly that. >>> >>> Best regards, >>> Grigory >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Fri, May 27, 2022 at 12:32 AM C.J. >>> <bi...@gm...> wrote: >>> >>> Hi, >>> >>> I run localrec in SCIPION v3.0.9 to extract >>> subparticles. But how can I export both >>> particles and metadata into relion3 star file >>> and particles? >>> >>> Thank you! >>> Jianhao >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> Untitled.png_______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Serban I. <SI...@ny...> - 2022-06-09 00:27:36
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Hi Jianhao, The vector considers as (0,0,0) the center of the particle box. Cheers, Serban ________________________________ From: C.J. <bi...@gm...> Sent: 08 June 2022 15:36 To: Mailing list for Scipion users <sci...@li...> Subject: [scipion-users] localrec: define subparticles - location vectors (px) Hi, I have a question about the vector in localrec, define subparticles, location vectors. If the vector defined by string. Is it based on the origin (0,0,0) in Chimera or the center of the particle box or something else? Thanks! Jianhao |
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From: C.J. <bi...@gm...> - 2022-06-08 22:20:47
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Hi, I followed the guide (https://github.com/I2PC/xmipp#standalone-installation) and install xmipp and link to scipion in scipion.conf. But there is some issue when launch scipion. $ scipion Scipion v3.0.9 - Eugenius The package scipion-pyworkflow is out of date. Your version is 3.0.18, the latest is 3.0.20. The package scipion-em is out of date. Your version is 3.0.13, the latest is 3.0.17. The package scipion-app is out of date. Your version is 3.0.9, the latest is 3.0.10. > error when importing from xmipp3.protocols: cannot import name 'setMRCSamplingRate' from 'pwem.convert.headers' (/data2/sw/scipion3/scipion-em/pwem/convert/headers.py) File "/data2/sw/xmipp/xmipp-bundle/src/scipion-em-xmipp/xmipp3/protocols/protocol_rotate_volume.py", line 30, in <module> Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue. There is still no xmipp in scipion GUI. Do I still miss anything? Thanks! Jianhao Alberto Garcia Mena <alb...@cn...> 于2022年6月6日周一 01:20写道： > Hi again, > > To install xmipp devel please follow this guide: > https://github.com/I2PC/xmipp#standalone-installation > On 4/6/22 1:08, C.J. wrote: > > Hi, I try to install xmipp but there is a question in the output log (see > attached picture). How can I response to the question? I can't click it or > type in the log. It's only a text display in the output log. > > Thanks! > Jianhao > > <jam...@gm...> 于2022年5月27日周五 15:23写道： > >> I think you need xmipp. emlib can point to that. >> >> Best wishes >> James >> >> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >> >> >> Hi, >> >> I have some issue (see the attached picture) while exporting particles. >> Did I miss something when installing SCIPION? >> >> Thanks! >> Jianhao >> >> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >> >>> Hi Jianhao, >>> >>> As Grigory pointed out, you can indeed run 'relion - export particles' >>> on the output of 'localrec - extract subparticles' to accomplish what you >>> want. >>> >>> Cheers, >>> Serban >>> ------------------------------ >>> *From:* C.J. <bi...@gm...> >>> *Sent:* 27 May 2022 13:18 >>> *To:* Mailing list for Scipion users < >>> sci...@li...> >>> *Subject:* Re: [scipion-users] export particles and metadata >>> >>> Hi, these particles are re-extracted by localrec. Soooo, i don't think >>> relion can do that. >>> >>> Jianhao >>> >>> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： >>> >>> Hi, >>> >>> I don't know about localrec plugin but relion plugin has an export >>> particle protocol that does exactly that. >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: >>> >>> Hi, >>> >>> I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I >>> export both particles and metadata into relion3 star file and particles? >>> >>> Thank you! >>> Jianhao >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> [image: Untitled.png]_______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > - Alberto GM - > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: C.J. <bi...@gm...> - 2022-06-08 19:37:00
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Hi, I have a question about the vector in localrec, define subparticles, location vectors. If the vector defined by string. Is it based on the origin (0,0,0) in Chimera or the center of the particle box or something else? Thanks! Jianhao |
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From: Carlos H. F. <car...@so...> - 2022-06-06 15:14:58
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Hello all! I hope that everybody is going well. I'm facing a problem with Deep Micrograph Cleaning. I have noticed that the Deep Micrograph Cleaning protocol has not performed any cleaning on my images. The particles in the images are the same before and after cleaning. Also, I've seen this warning in the log: WARNING:tensorflow:From /home/impmc/anaconda3/envs/xmipp_MicCleaner/lib/python3.6/site-packages/tensorflow/python/ops/init_ops.py:87: calling VarianceScaling.__init__ (from tensorflow.python.ops.init_ops) with distribution=normal is deprecated and will be removed in a future version. 00005: Instructions for updating: 00006: `normal` is a deprecated alias for `truncated_normal` 00007: WARNING:tensorflow:No training configuration found in save file: the model was *not* compiled. Compile it manually. 00008: WARNING:tensorflow:No training configuration found in save file: the model was *not* compiled. Compile it manually. Is this warning related to Deep Micrograph Cleaning protocol malfunction ? Thanks in advance! Best regards, Carlos Fernandes. |
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From: Alberto G. M. <alb...@cn...> - 2022-06-06 08:19:15
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Hi again, To install xmipp devel please follow this guide: https://github.com/I2PC/xmipp#standalone-installation On 4/6/22 1:08, C.J. wrote: > Hi, I try to install xmipp but there is a question in the output log > (see attached picture). How can I response to the question? I can't > click it or type in the log. It's only a text display in the output log. > > Thanks! > Jianhao > > <jam...@gm...> 于2022年5月27日周五 15:23写道： > > I think you need xmipp. emlib can point to that. > > Best wishes > James > >> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >> >> >> Hi, >> >> I have some issue (see the attached picture) while exporting >> particles. Did I miss something when installing SCIPION? >> >> Thanks! >> Jianhao >> >> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >> >> Hi Jianhao, >> >> As Grigory pointed out, you can indeed run 'relion - export >> particles' on the output of 'localrec - extract subparticles' >> to accomplish what you want. >> >> Cheers, >> Serban >> ------------------------------------------------------------------------ >> *From:* C.J. <bi...@gm...> >> *Sent:* 27 May 2022 13:18 >> *To:* Mailing list for Scipion users >> <sci...@li...> >> *Subject:* Re: [scipion-users] export particles and metadata >> Hi, these particles are re-extracted by localrec. Soooo, i >> don't think relion can do that. >> >> Jianhao >> >> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 >> 02:26写道： >> >> Hi, >> >> I don't know about localrec plugin but relion plugin has >> an export particle protocol that does exactly that. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> >> wrote: >> >> Hi, >> >> I run localrec in SCIPION v3.0.9 to extract >> subparticles. But how can I export both particles and >> metadata into relion3 star file and particles? >> >> Thank you! >> Jianhao >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> Untitled.png_______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: Alberto G. M. <alb...@cn...> - 2022-06-06 08:15:55
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Hello Jianhao, You just have to write YES (or press Enter) or no. Is safer to ptype no and generate a new config file '/./xmipp config/' Thanks On 4/6/22 1:08, C.J. wrote: > Hi, I try to install xmipp but there is a question in the output log > (see attached picture). How can I response to the question? I can't > click it or type in the log. It's only a text display in the output log. > > Thanks! > Jianhao > > <jam...@gm...> 于2022年5月27日周五 15:23写道： > > I think you need xmipp. emlib can point to that. > > Best wishes > James > >> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >> >> >> Hi, >> >> I have some issue (see the attached picture) while exporting >> particles. Did I miss something when installing SCIPION? >> >> Thanks! >> Jianhao >> >> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >> >> Hi Jianhao, >> >> As Grigory pointed out, you can indeed run 'relion - export >> particles' on the output of 'localrec - extract subparticles' >> to accomplish what you want. >> >> Cheers, >> Serban >> ------------------------------------------------------------------------ >> *From:* C.J. <bi...@gm...> >> *Sent:* 27 May 2022 13:18 >> *To:* Mailing list for Scipion users >> <sci...@li...> >> *Subject:* Re: [scipion-users] export particles and metadata >> Hi, these particles are re-extracted by localrec. Soooo, i >> don't think relion can do that. >> >> Jianhao >> >> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 >> 02:26写道： >> >> Hi, >> >> I don't know about localrec plugin but relion plugin has >> an export particle protocol that does exactly that. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> >> wrote: >> >> Hi, >> >> I run localrec in SCIPION v3.0.9 to extract >> subparticles. But how can I export both particles and >> metadata into relion3 star file and particles? >> >> Thank you! >> Jianhao >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> Untitled.png_______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- - Alberto GM - |
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From: C.J. <bi...@gm...> - 2022-06-03 23:08:52
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Hi, I try to install xmipp but there is a question in the output log (see attached picture). How can I response to the question? I can't click it or type in the log. It's only a text display in the output log. Thanks! Jianhao <jam...@gm...> 于2022年5月27日周五 15:23写道： > I think you need xmipp. emlib can point to that. > > Best wishes > James > > On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: > > > Hi, > > I have some issue (see the attached picture) while exporting particles. > Did I miss something when installing SCIPION? > > Thanks! > Jianhao > > Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： > >> Hi Jianhao, >> >> As Grigory pointed out, you can indeed run 'relion - export particles' on >> the output of 'localrec - extract subparticles' to accomplish what you want. >> >> Cheers, >> Serban >> ------------------------------ >> *From:* C.J. <bi...@gm...> >> *Sent:* 27 May 2022 13:18 >> *To:* Mailing list for Scipion users <sci...@li... >> > >> *Subject:* Re: [scipion-users] export particles and metadata >> >> Hi, these particles are re-extracted by localrec. Soooo, i don't think >> relion can do that. >> >> Jianhao >> >> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： >> >> Hi, >> >> I don't know about localrec plugin but relion plugin has an export >> particle protocol that does exactly that. >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: >> >> Hi, >> >> I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I >> export both particles and metadata into relion3 star file and particles? >> >> Thank you! >> Jianhao >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > [image: Untitled.png]_______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2022-05-31 13:40:08
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Dear Hongchen Fan! Scipion tomography functionality is still in beta (not released). We are currently moving from relion3 to relion4, so relion3 functionality is almost deprecated. Yes relion4 can be used (in beta) in Scipion3. I'm afraid I can not answer your very detailed questions. If you are willing to deep into tomography using Scipion, we can facilitate access to our slack workspace upon request (just email me). There you can join developers and other betatesters where hopefully can answer your questions. On 30/5/22 15:27, 范宏成 wrote: > Dear all, > I am new to the cryo-EM tomography. I have some questions when using > some softwares. > 1. I watched subtomogram-averaging videos using relion3 on the > scipion3 website. I noticed that adding extra restraints like > --sigma_tilt 3, --sigma_psi 3 in relion-3d classification maybe in > order to improve the alignment accuracy. I wanna know whether these > values (--sigma_tilt 3, --sigma_psi 3) are generally applicable. For > subtomogram-averaging analysis, what is the ordinary range of these > values when using the relion-3d classification? I recently tried the > relion4 too. I found that the relion4 tomo-processing strategy > (pseudo-subtomograms) showed much difference from the relion3. I'm not > sure whether I need to add these extra retraints in relion4-3d > classification or not. > > 2. Does relion4 can be used in the Scipion3 now？I noticed the tilt > handedness parameter in the relion_tomo_import_tomograms protocol. > The default values is -1. I wanna know the influence of this > parameter for subtomo-averaging and which condition to choose the > value of 1 . I found that I could also got same chirality androughly > same resolution 3D structure when I chose the 1 for the tilt > handedness parameter. > > 3. How to manually judge the alignment accuracy of particles when > doing the sub-tomogram analysis in Scipion. There existed some > mis-oriented particles after relion-refinement. Can I put these > aligned particles to original tomograms to check which particles are > mis-oriented and thus I can manually changed their relevant euler > angles to make them better fit the geometric constraint in tomograms > or just deleted them. > > 4.I recently tried the Aretomo (v1.1.0) for my project(FIB-milled). I > found better tomography reconstruction in aretomo compared to using > imod patch-tracking in my project. I am wondering whether aretomo > results can be better than imod even using the sub-tilt refinement in > relion4 ? Dose anyone test the performance of aretomo for > subtomo-averaing? > > 5. I am doing the tomogram segmentation. My tomogram have some > microstructures like mitochondrion, ribosome, microtubule, lipid > droplets, endoplasmic reticulum. Are there some softwares recommended > or worth a try ? > > Looking forward to your response. Thank you！ > > > Hongcheng Fan > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: 范宏成 <187...@16...> - 2022-05-30 13:27:41
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Dear all, I am new to the cryo-EM tomography. I have some questions when using some softwares. 1. I watched subtomogram-averaging videos using relion3 on the scipion3 website. I noticed that adding extra restraints like --sigma_tilt 3, --sigma_psi 3 in relion-3d classification maybe in order to improve the alignment accuracy. I wanna know whether these values (--sigma_tilt 3, --sigma_psi 3) are generally applicable. For subtomogram-averaging analysis, what is the ordinary range of these values when using the relion-3d classification? I recently tried the relion4 too. I found that the relion4 tomo-processing strategy (pseudo-subtomograms) showed much difference from the relion3. I'm not sure whether I need to add these extra retraints in relion4-3d classification or not. 2. Does relion4 can be used in the Scipion3 now？I noticed the tilt handedness parameter in the relion_tomo_import_tomograms protocol. The default values is -1. I wanna know the influence of this parameter for subtomo-averaging and which condition to choose the value of 1 . I found that I could also got same chirality and roughly same resolution 3D structure when I chose the 1 for the tilt handedness parameter. 3. How to manually judge the alignment accuracy of particles when doing the sub-tomogram analysis in Scipion. There existed some mis-oriented particles after relion-refinement. Can I put these aligned particles to original tomograms to check which particles are mis-oriented and thus I can manually changed their relevant euler angles to make them better fit the geometric constraint in tomograms or just deleted them. 4.I recently tried the Aretomo (v1.1.0) for my project(FIB-milled). I found better tomography reconstruction in aretomo compared to using imod patch-tracking in my project. I am wondering whether aretomo results can be better than imod even using the sub-tilt refinement in relion4 ? Dose anyone test the performance of aretomo for subtomo-averaing? 5. I am doing the tomogram segmentation. My tomogram have some microstructures like mitochondrion, ribosome, microtubule, lipid droplets, endoplasmic reticulum. Are there some softwares recommended or worth a try ? Looking forward to your response. Thank you！ Hongcheng Fan |
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From: Pablo C. <pc...@cn...> - 2022-05-28 16:52:29
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Hi! Do you see any error message in your terminal when opening Scipion? On 27/5/22 23:52, C.J. wrote: > Hi, > > I have some issue (see the attached picture) while exporting > particles. Did I miss something when installing SCIPION? > > Thanks! > Jianhao > > Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： > > Hi Jianhao, > > As Grigory pointed out, you can indeed run 'relion - export > particles' on the output of 'localrec - extract subparticles' to > accomplish what you want. > > Cheers, > Serban > ------------------------------------------------------------------------ > *From:* C.J. <bi...@gm...> > *Sent:* 27 May 2022 13:18 > *To:* Mailing list for Scipion users > <sci...@li...> > *Subject:* Re: [scipion-users] export particles and metadata > Hi, these particles are re-extracted by localrec. Soooo, i don't > think relion can do that. > > Jianhao > > Grigory Sharov <sha...@gm...> 于2022年5月27日周五 > 02:26写道： > > Hi, > > I don't know about localrec plugin but relion plugin has an > export particle protocol that does exactly that. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > > > On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: > > Hi, > > I run localrec in SCIPION v3.0.9 to extract subparticles. > But how can I export both particles and metadata into > relion3 star file and particles? > > Thank you! > Jianhao > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: <jam...@gm...> - 2022-05-27 22:22:55
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I think you need xmipp. emlib can point to that. Best wishes James > On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: > > > Hi, > > I have some issue (see the attached picture) while exporting particles. Did I miss something when installing SCIPION? > > Thanks! > Jianhao > > Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >> Hi Jianhao, >> >> As Grigory pointed out, you can indeed run 'relion - export particles' on the output of 'localrec - extract subparticles' to accomplish what you want. >> >> Cheers, >> Serban >> From: C.J. <bi...@gm...> >> Sent: 27 May 2022 13:18 >> To: Mailing list for Scipion users <sci...@li...> >> Subject: Re: [scipion-users] export particles and metadata >> >> Hi, these particles are re-extracted by localrec. Soooo, i don't think relion can do that. >> >> Jianhao >> >> Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： >> Hi, >> >> I don't know about localrec plugin but relion plugin has an export particle protocol that does exactly that. >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 >> e-mail: gs...@mr... >> >> >> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: >> Hi, >> >> I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I export both particles and metadata into relion3 star file and particles? >> >> Thank you! >> Jianhao >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: C.J. <bi...@gm...> - 2022-05-27 21:53:17
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Hi, I have some issue (see the attached picture) while exporting particles. Did I miss something when installing SCIPION? Thanks! Jianhao Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： > Hi Jianhao, > > As Grigory pointed out, you can indeed run 'relion - export particles' on > the output of 'localrec - extract subparticles' to accomplish what you want. > > Cheers, > Serban > ------------------------------ > *From:* C.J. <bi...@gm...> > *Sent:* 27 May 2022 13:18 > *To:* Mailing list for Scipion users <sci...@li...> > *Subject:* Re: [scipion-users] export particles and metadata > > Hi, these particles are re-extracted by localrec. Soooo, i don't think > relion can do that. > > Jianhao > > Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： > > Hi, > > I don't know about localrec plugin but relion plugin has an export > particle protocol that does exactly that. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: > > Hi, > > I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I > export both particles and metadata into relion3 star file and particles? > > Thank you! > Jianhao > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Serban I. <SI...@ny...> - 2022-05-27 19:14:22
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Hi Jianhao, As Grigory pointed out, you can indeed run 'relion - export particles' on the output of 'localrec - extract subparticles' to accomplish what you want. Cheers, Serban ________________________________ From: C.J. <bi...@gm...> Sent: 27 May 2022 13:18 To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] export particles and metadata Hi, these particles are re-extracted by localrec. Soooo, i don't think relion can do that. Jianhao Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> 于2022年5月27日周五 02:26写道： Hi, I don't know about localrec plugin but relion plugin has an export particle protocol that does exactly that. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...<mailto:bi...@gm...>> wrote: Hi, I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I export both particles and metadata into relion3 star file and particles? Thank you! Jianhao _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: C.J. <bi...@gm...> - 2022-05-27 17:19:07
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Hi, these particles are re-extracted by localrec. Soooo, i don't think relion can do that. Jianhao Grigory Sharov <sha...@gm...> 于2022年5月27日周五 02:26写道： > Hi, > > I don't know about localrec plugin but relion plugin has an export > particle protocol that does exactly that. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: > >> Hi, >> >> I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I >> export both particles and metadata into relion3 star file and particles? >> >> Thank you! >> Jianhao >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Grigory S. <sha...@gm...> - 2022-05-27 09:25:56
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Hi, I don't know about localrec plugin but relion plugin has an export particle protocol that does exactly that. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, May 27, 2022 at 12:32 AM C.J. <bi...@gm...> wrote: > Hi, > > I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I > export both particles and metadata into relion3 star file and particles? > > Thank you! > Jianhao > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: C.J. <bi...@gm...> - 2022-05-26 23:32:10
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Hi, I run localrec in SCIPION v3.0.9 to extract subparticles. But how can I export both particles and metadata into relion3 star file and particles? Thank you! Jianhao |
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From: Grigory S. <sha...@gm...> - 2022-05-21 16:52:44
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Hi, I don't really use cryosparc, so can't comment on the first issue. As for the second problem you are right, there's currently no way to do this in scipion. I've made a pull request <https://github.com/scipion-em/scipion-em/pull/333> which allows to assign ctf from a second (identical) set of particles, but this won't be released until the next merge window. You could try it by manually applying https://patch-diff.githubusercontent.com/raw/scipion-em/scipion-em/pull/333.diff to pwem/protocols/protocol_ctf_assign.py file (make a backup copy first!). Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, May 20, 2022 at 3:39 PM Kumpula, Esa-Pekka < esa...@he...> wrote: > Hi all, > > > > I have two issues when importing particles from cryosparc to scipion. > > I did initial processing steps in cryosparc (using patch motion > correction) and have now successfully imported the particles as well as the > associated micrographs into scipion (by running csparc2star.py and then > importing using the .star file). The issue then is that all the micrographs > and particles look very noisy in scipion, but if I reconstruct I get a > reasonable map. If I run extract coordinates and look at the micrographs > from there, they look as they should so I think they are essentially ok. > > > > The issue is that when I run subtract projection, I get negative density > for the remaining part, which suggests to me that there is some issue with > the particles, possibly normalization. > > > > So what I would think to do is to re-extract the particles using relion’s > extraction protocol to get the normalization correct. The issue is that I > don’t know how to transfer the previously refined ctf parameters of the > particles that I imported into these new particles to avoid re-running ctf > estimation and later per-particle ctf refinement. The particles I imported > have these parameters after import, but they are not a SetOfCtf type that I > could use as input for relion particle extraction or assign ctf. > > > > Any pointers? I have a slightly older Scipion version (3.0.8) so if this > is not an issue with current releases then I’m happy to update. > > > > Cheers, > > EP > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Kumpula, Esa-P. <esa...@he...> - 2022-05-20 14:39:09
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Hi all, I have two issues when importing particles from cryosparc to scipion. I did initial processing steps in cryosparc (using patch motion correction) and have now successfully imported the particles as well as the associated micrographs into scipion (by running csparc2star.py and then importing using the .star file). The issue then is that all the micrographs and particles look very noisy in scipion, but if I reconstruct I get a reasonable map. If I run extract coordinates and look at the micrographs from there, they look as they should so I think they are essentially ok. The issue is that when I run subtract projection, I get negative density for the remaining part, which suggests to me that there is some issue with the particles, possibly normalization. So what I would think to do is to re-extract the particles using relion’s extraction protocol to get the normalization correct. The issue is that I don’t know how to transfer the previously refined ctf parameters of the particles that I imported into these new particles to avoid re-running ctf estimation and later per-particle ctf refinement. The particles I imported have these parameters after import, but they are not a SetOfCtf type that I could use as input for relion particle extraction or assign ctf. Any pointers? I have a slightly older Scipion version (3.0.8) so if this is not an issue with current releases then I’m happy to update. Cheers, EP |
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From: Matt H. <ma...@ms...> - 2022-04-29 17:33:15
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On Fri, Apr 29, 2022 at 2:00 AM Alberto Garcia Mena <
alb...@cn...> wrote:
> I tried to install xmipp in Ubuntu 22.04 from scratch and I get an error
> like "undefined reference to 'std::...". By default Ubuntu installed gcc-11
> ( sudo apt build-essential). I installed gcc/g++-10, updated the symbolic
> links and removed and reinstalled libopenmpi-dev. After that, I was able to
> install Xmipp successively.
>
Yes, those are the errors I got with GCC 11.2.0, the default version in
Ubuntu 22.04. For example:
<artificial>:(.text+0x4e86): undefined reference to
> `std::__throw_bad_array_new_length()'
> /usr/bin/ld: lib/libXmipp.so: undefined reference to
> `std::__exception_ptr::exception_ptr::_M_release()'
> /usr/bin/ld: lib/libXmipp.so: undefined reference to
> `std::__exception_ptr::exception_ptr::_M_addref()'
> collect2: error: ld returned 1 exit status
> scons: *** [bin/xmipp_micrograph_scissor] Error 1
> scons: building terminated because of errors.
Some error occurred during the compilation of 'xmipp'
> ('bin/xmipp_micrograph_scissor').
Good to know that it works with GCC 10. We had a facility maintenance
window overlap with the release of Ubuntu 22.04, so I did the upgrade last
week. I reverted to 20.04 yesterday because I was in a hurry. I'll
revisit this during the next maintenance window, but that won't be for a
long time.
It's curious that the linker couldn't find parts of the standard library
related to exceptions, but presumably the linker could find the rest of the
standard library such as the ubiquitous std::vector.
Matt
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