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From: Pablo C. <pc...@cn...> - 2021-04-15 11:26:33
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I think we had that before but was killing the performance. Obviously can be rescued at expense of time. On 15/4/21 11:19, Grigory Sharov wrote: > I think it would be good to check each movie header on import as e.g. > in cryosparc, to detect corrupted movies before they enter the pipeline. > > 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 Thu, Apr 15, 2021 at 8:45 AM Carlos Oscar Sorzano <co...@cn... > <mailto:co...@cn...>> wrote: > > Dear all, > > El 14/04/2021 a las 22:33, Grigory Sharov escribió: >> Hi Matt, >> >> Thank you! I see two errors: >> >> /bin/sh: 1: >> /programs/x86_64-linux/scipion/3.0.0/software/em/eman-2.31/bin/e2proc2d.py: >> not found >> IndexError: list index out of range >> >> First one happened since you have probably asked to create >> thumbnails (which require eman2), while the second one indicates >> that you have a movie with less frames than expected. >> Try running "scipion installp -p scipion-em-motioncorr --noBin". >> This will update ther plugin to the latest version where it does >> not crash if eman is not found. Also it will print the corrupted >> movie name with less frames. > > If this is a situation that happens from time to time, could we > make the frame alignment call to be aware of this possibility and > count the effective number of frames for each movie before calling > the alignment program? > > Kind regards, Carlos Oscar > >> >> 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...> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <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: Grigory S. <sha...@gm...> - 2021-04-15 09:20:15
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I think it would be good to check each movie header on import as e.g. in cryosparc, to detect corrupted movies before they enter the pipeline. 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 Thu, Apr 15, 2021 at 8:45 AM Carlos Oscar Sorzano <co...@cn...> wrote: > Dear all, > El 14/04/2021 a las 22:33, Grigory Sharov escribió: > > Hi Matt, > > Thank you! I see two errors: > > /bin/sh: 1: > /programs/x86_64-linux/scipion/3.0.0/software/em/eman-2.31/bin/e2proc2d.py: > not found > IndexError: list index out of range > > First one happened since you have probably asked to create thumbnails > (which require eman2), while the second one indicates that you have a movie > with less frames than expected. > Try running "scipion installp -p scipion-em-motioncorr --noBin". This will > update ther plugin to the latest version where it does not crash if eman is > not found. Also it will print the corrupted movie name with less frames. > > If this is a situation that happens from time to time, could we make the > frame alignment call to be aware of this possibility and count the > effective number of frames for each movie before calling the alignment > program? > > Kind regards, Carlos Oscar > > > 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... > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Grigory S. <sha...@gm...> - 2021-04-15 08:30:54
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Hi Dmitry, As usual, you need to make sure coord file names match micrograph names. Unfortunately, import coordinates from scipion sqlite was never implemented. 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 Thu, Apr 15, 2021 at 9:26 AM Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > > > To save disc space, I would like to extract my already processed > particles' coordinates and re-import them back into the project. That step > will allow me to delete many of the intermediate protocols. > > For that, I use the Import coordinates protocol > > As input, I use the folder with the required coordinates and the > micrographs in my project. > > But I get the empty output file with 0 coordinates imported. > > > Could you please prompt me on how can I import the coordinates correctly? > > > > > > Thank you > > > > Sincerely, > > Dmitry > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-04-15 08:26:06
|
<>Dear colleagues, To save disc space, I would like to extract my already processed particles' coordinates and re-import them back into the project. That step will allow me to delete many of the intermediate protocols. For that, I use the Import coordinates protocol As input, I use the folder with the required coordinates and the micrographs in my project. But I get the empty output file with 0 coordinates imported. Could you please prompt me on how can I import the coordinates correctly? Thank you Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2021-04-15 07:58:38
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Hi Dmitry, El 15/04/2021 a las 9:53, Dmitry Semchonok escribió: > Dear Carlos Oscar, > > Do I understand correctly that if I already have the processed > particles file (after 2D/3D classification) I can extract the > coordinates and use them for Deep consensus picking protocol? > This can certainly be a way. Actually, we never tested to input a picking and a cleaner (after 2D and 3D classification) version of that picking, but it makes sense. > Or do you mean to start picking form the beginning? Not necessarily, you may use what you already have. Cheers, Carlos Oscar > > > Thank you > > Sincerely, > Dmitry > > > > > >> On 15. Apr 2021, at 09:46, Carlos Oscar Sorzano <co...@cn... >> <mailto:co...@cn...>> wrote: >> >> The deep consensus is a much better way of getting rid of coordinates >> that do not point to useful particles. >> >> Kind regards, Carlos Oscar >> >> El 14/04/2021 a las 23:03, Grigory Sharov escribió: >>> Hi, >>> >>> The relion command is only useful for finding particles with all >>> zeros, so it won't help to find noise particles. You could try xmipp >>> - screen particles with Z-score sorting. >>> >>> 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 Wed, Apr 14, 2021 at 9:55 PM Dmitry A. Semchonok >>> <sem...@gm... <mailto:sem...@gm...>> wrote: >>> >>> Dear Carlos Oscar & Grigory, >>> >>> >>> Indeed, by empty particles I mean the projections that contain >>> no information about studying sample – so the noised ones, not >>> the ones with the ice (the default value in abovemention xmipp >>> protocol it is 1.1). >>> >>> >>> The problem I am tackling is the presence of many empty picked >>> positions that somehow doesn’t classified out after 2D/3D. >>> >>> >>> So I understood that I can measure the threshold with relion >>> script that you pointed out. >>> >>> >>> And I will try to pick better 😊 >>> >>> >>> Thank you both >>> >>> >>> Kind regards, >>> >>> Dmitry >>> >>> >>> >>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> >>> for Windows 10 >>> >>> >>> *From: *Grigory Sharov <mailto:sha...@gm...> >>> *Sent: *Wednesday, April 14, 2021 3:39 PM >>> *To: *Mailing list for Scipion users >>> <mailto:sci...@li...> >>> *Subject: *Re: [scipion-users] Removing empty particles >>> >>> >>> Hi Dmitry, >>> >>> >>> I haven't used that protocol so can't comment on it. By empty >>> particles do you mean completely black particles with 0.0 or >>> some particles with noise inside? You could use >>> relion_image_handler with the "--stats" option to find the >>> former ones. >>> >>> >>> Getting rid of second ones is more difficult. >>> >>> >>> 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok >>> <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> >>> Dear colleagues, >>> >>> >>> One more question about effective deletion of the empty >>> particles in the dataset. >>> >>> Correct me if I am wrong, but the dedicated tools for that >>> purpose are: xmipp - eliminate empty classes // particles. >>> >>> I would like to ask if there is a possibility to boost the >>> processing speed of them? I am afraid that it is using only 1 >>> MPI and in case of few millions particles the processing on 1 >>> MPI can take few days. >>> >>> >>> Thank you >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> <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... >> <mailto: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: Dmitry S. <Sem...@gm...> - 2021-04-15 07:53:16
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Dear Carlos Oscar, Do I understand correctly that if I already have the processed particles file (after 2D/3D classification) I can extract the coordinates and use them for Deep consensus picking protocol? Or do you mean to start picking form the beginning? Thank you Sincerely, Dmitry > On 15. Apr 2021, at 09:46, Carlos Oscar Sorzano <co...@cn...> wrote: > > The deep consensus is a much better way of getting rid of coordinates that do not point to useful particles. > > Kind regards, Carlos Oscar > > El 14/04/2021 a las 23:03, Grigory Sharov escribió: >> Hi, >> >> The relion command is only useful for finding particles with all zeros, so it won't help to find noise particles. You could try xmipp - screen particles with Z-score sorting. >> >> 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 Wed, Apr 14, 2021 at 9:55 PM Dmitry A. Semchonok <sem...@gm... <mailto:sem...@gm...>> wrote: >> Dear Carlos Oscar & Grigory, >> >> >> Indeed, by empty particles I mean the projections that contain no information about studying sample – so the noised ones, not the ones with the ice (the default value in abovemention xmipp protocol it is 1.1). >> >> >> The problem I am tackling is the presence of many empty picked positions that somehow doesn’t classified out after 2D/3D. >> >> >> So I understood that I can measure the threshold with relion script that you pointed out. >> >> >> And I will try to pick better 😊 >> >> >> Thank you both >> >> >> Kind regards, >> >> Dmitry >> >> >> >> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 >> >> >> From: Grigory Sharov <mailto:sha...@gm...> >> Sent: Wednesday, April 14, 2021 3:39 PM >> To: Mailing list for Scipion users <mailto:sci...@li...> >> Subject: Re: [scipion-users] Removing empty particles >> >> >> Hi Dmitry, >> >> >> I haven't used that protocol so can't comment on it. By empty particles do you mean completely black particles with 0.0 or some particles with noise inside? You could use relion_image_handler with the "--stats" option to find the former ones. >> >> >> Getting rid of second ones is more difficult. >> >> >> >> 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> >> Dear colleagues, >> >> >> One more question about effective deletion of the empty particles in the dataset. >> >> Correct me if I am wrong, but the dedicated tools for that purpose are: xmipp - eliminate empty classes // particles. >> >> I would like to ask if there is a possibility to boost the processing speed of them? I am afraid that it is using only 1 MPI and in case of few millions particles the processing on 1 MPI can take few days. >> >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <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 <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: Carlos O. S. <co...@cn...> - 2021-04-15 07:47:09
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The deep consensus is a much better way of getting rid of coordinates that do not point to useful particles. Kind regards, Carlos Oscar El 14/04/2021 a las 23:03, Grigory Sharov escribió: > Hi, > > The relion command is only useful for finding particles with all > zeros, so it won't help to find noise particles. You could try xmipp - > screen particles with Z-score sorting. > > 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 Wed, Apr 14, 2021 at 9:55 PM Dmitry A. Semchonok > <sem...@gm... <mailto:sem...@gm...>> wrote: > > Dear Carlos Oscar & Grigory, > > Indeed, by empty particles I mean the projections that contain no > information about studying sample – so the noised ones, not the > ones with the ice (the default value in abovemention xmipp > protocol it is 1.1). > > The problem I am tackling is the presence of many empty picked > positions that somehow doesn’t classified out after 2D/3D. > > So I understood that I can measure the threshold with relion > script that you pointed out. > > And I will try to pick better 😊 > > Thank you both > > Kind regards, > > Dmitry > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> > for Windows 10 > > *From: *Grigory Sharov <mailto:sha...@gm...> > *Sent: *Wednesday, April 14, 2021 3:39 PM > *To: *Mailing list for Scipion users > <mailto:sci...@li...> > *Subject: *Re: [scipion-users] Removing empty particles > > Hi Dmitry, > > I haven't used that protocol so can't comment on it. By empty > particles do you mean completely black particles with 0.0 or some > particles with noise inside? You could use relion_image_handler > with the "--stats" option to find the former ones. > > Getting rid of second ones is more difficult. > > > 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok > <Sem...@gm... <mailto:Sem...@gm...>> wrote: > > Dear colleagues, > > > One more question about effective deletion of the empty particles > in the dataset. > > Correct me if I am wrong, but the dedicated tools for that purpose > are: xmipp - eliminate empty classes // particles. > > I would like to ask if there is a possibility to boost the > processing speed of them? I am afraid that it is using only 1 MPI > and in case of few millions particles the processing on 1 MPI can > take few days. > > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <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: Carlos O. S. <co...@cn...> - 2021-04-15 07:45:44
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Dear all, El 14/04/2021 a las 22:33, Grigory Sharov escribió: > Hi Matt, > > Thank you! I see two errors: > > /bin/sh: 1: > /programs/x86_64-linux/scipion/3.0.0/software/em/eman-2.31/bin/e2proc2d.py: > not found > IndexError: list index out of range > > First one happened since you have probably asked to create thumbnails > (which require eman2), while the second one indicates that you have a > movie with less frames than expected. > Try running "scipion installp -p scipion-em-motioncorr --noBin". This > will update ther plugin to the latest version where it does not crash > if eman is not found. Also it will print the corrupted movie name with > less frames. If this is a situation that happens from time to time, could we make the frame alignment call to be aware of this possibility and count the effective number of frames for each movie before calling the alignment program? Kind regards, Carlos Oscar > > 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...> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2021-04-15 07:43:08
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We suspect that there might be a problem with the access to GPUs in streaming (the steps would need to be queued somehow). Do you think this could be the case? As Grigory says, it would be helpful to see the whole stdout.txt file to check if there is any clue about the error cause. Kind regards, Carlos Oscar El 14/04/2021 a las 22:21, Matt Harrington via scipion-users escribió: > On Wed, Apr 14, 2021 at 1:05 PM Grigory Sharov > <sha...@gm... <mailto:sha...@gm...>> wrote: > > Could you attach run.stdout here? Are you running in streaming? > How many threads did you use? What did you put in the GPU IDs field? > > > I emailed you a bunch of logs directly. > > 9 threads. 8 GPUs listed 0 - 7 in the GPU ID field. > > Re: streaming mode. We usually operate that way and process > on-the-fly, but on this new system (which never ran Scipion 2) we're > processing movies that were previously collected. > > Matt > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-04-14 21:03:27
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Hi, The relion command is only useful for finding particles with all zeros, so it won't help to find noise particles. You could try xmipp - screen particles with Z-score sorting. 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 Wed, Apr 14, 2021 at 9:55 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear Carlos Oscar & Grigory, > > > > Indeed, by empty particles I mean the projections that contain no > information about studying sample – so the noised ones, not the ones with > the ice (the default value in abovemention xmipp protocol it is 1.1). > > > > The problem I am tackling is the presence of many empty picked positions > that somehow doesn’t classified out after 2D/3D. > > > > So I understood that I can measure the threshold with relion script that > you pointed out. > > > > And I will try to pick better 😊 > > > > Thank you both > > > > Kind regards, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Grigory Sharov <sha...@gm...> > *Sent: *Wednesday, April 14, 2021 3:39 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] Removing empty particles > > > > Hi Dmitry, > > > > I haven't used that protocol so can't comment on it. By empty particles do > you mean completely black particles with 0.0 or some particles with noise > inside? You could use relion_image_handler with the "--stats" option to > find the former ones. > > > > Getting rid of second ones is more difficult. > > > 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> > wrote: > > Dear colleagues, > > > One more question about effective deletion of the empty particles in the > dataset. > > Correct me if I am wrong, but the dedicated tools for that purpose are: > xmipp - eliminate empty classes // particles. > > I would like to ask if there is a possibility to boost the processing > speed of them? I am afraid that it is using only 1 MPI and in case of few > millions particles the processing on 1 MPI can take few days. > > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > |
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From: Dmitry A. S. <sem...@gm...> - 2021-04-14 20:55:54
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Dear Carlos Oscar & Grigory,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Indeed, by empty particles I mean the projections that contain no information about studying sample – so the noised ones, not the ones with the ice (the default value in abovemention xmipp protocol it is 1.1).</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The problem I am tackling is the presence of many empty picked positions that somehow doesn’t classified out after 2D/3D.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>So I understood that I can measure the threshold with relion script that you pointed out.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>And I will try to pick better <span style='font-family:"Segoe UI Emoji",sans-serif'>😊</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you both</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Kind regards,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:sha...@gm...">Grigory Sharov</a><br><b>Sent: </b>Wednesday, April 14, 2021 3:39 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Removing empty particles</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Dmitry,</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I haven't used that protocol so can't comment on it. By empty particles do you mean completely black particles with 0.0 or some particles with noise inside? You could use relion_image_handler with the "--stats" option to find the former ones. </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Getting rid of second ones is more difficult.</p></div><div><p class=MsoNormal><br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <<a href="mailto:Sem...@gm..." target="_blank">Sem...@gm...</a>> wrote:</p></div></div><p class=MsoNormal style='margin-left:4.8pt'>Dear colleagues,<br><br><br>One more question about effective deletion of the empty particles in the dataset.<br><br>Correct me if I am wrong, but the dedicated tools for that purpose are: xmipp - eliminate empty classes // particles.<br><br>I would like to ask if there is a possibility to boost the processing speed of them? I am afraid that it is using only 1 MPI and in case of few millions particles the processing on 1 MPI can take few days.<br><br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
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From: Grigory S. <sha...@gm...> - 2021-04-14 20:33:35
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Hi Matt, Thank you! I see two errors: /bin/sh: 1: /programs/x86_64-linux/scipion/3.0.0/software/em/eman-2.31/bin/e2proc2d.py: not found IndexError: list index out of range First one happened since you have probably asked to create thumbnails (which require eman2), while the second one indicates that you have a movie with less frames than expected. Try running "scipion installp -p scipion-em-motioncorr --noBin". This will update ther plugin to the latest version where it does not crash if eman is not found. Also it will print the corrupted movie name with less frames. 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... |
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From: Matt H. <ma...@ms...> - 2021-04-14 20:22:12
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On Wed, Apr 14, 2021 at 1:05 PM Grigory Sharov <sha...@gm...> wrote: > Could you attach run.stdout here? Are you running in streaming? How many > threads did you use? What did you put in the GPU IDs field? > I emailed you a bunch of logs directly. 9 threads. 8 GPUs listed 0 - 7 in the GPU ID field. Re: streaming mode. We usually operate that way and process on-the-fly, but on this new system (which never ran Scipion 2) we're processing movies that were previously collected. Matt |
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From: Grigory S. <sha...@gm...> - 2021-04-14 20:05:38
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Hi Matt, Could you attach run.stdout here? Are you running in streaming? How many threads did you use? What did you put in the GPU IDs field? 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 Wed, Apr 14, 2021 at 8:56 PM Matt Harrington via scipion-users < sci...@li...> wrote: > > We use Scipion 3 to read in 2000+ micrographs and process them with > motioncor2. Scipion 3 seems to stop processing after anywhere from 10 - > 500 movies. Error below. > > This worked fine under Scipion 2. We don't think we've made any changes > to our workflow. > > Any ideas? > > 00309: 2021-04-08 17:43:08,289 INFO: STARTED: processMovieStep, step > 561, time 2021-04-08 17:43:08.288900 > 00310: 2021-04-08 17:43:08,302 INFO: Processing movie: > Runs/000790_ProtMotionCorr/tmp/movie_000560/dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11.tif > 00311: 2021-04-08 17:43:08,304 INFO: > /programs/x86_64-linux/scipion/3.0.0/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101 > -InTiff "dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11.tif" -OutMrc > "../../extra/dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11_aligned_mic.mrc" > -Patch 7 5 -MaskCent 0 0 -MaskSize 1 1 -FtBin 2.0 -Tol 0.5 -Group 1 -FmDose > 0.67 -Throw 1 -Trunc 0 -PixSize 0.1865 -kV 200.0 -LogFile > ../../extra/micrograph_000560_ -InitDose 0.0 -OutStack 0 -Mag 1.000 1.000 > 0.000 -Gain "/msg/data6/scratch/Gain-Refs/K3-GainRefx1m3_20210405.mrc" > -RotGain 0 -FlipGain 0 -Gpu 6 -SumRange 0.0 0.0 -InFmMotion 1 > 00312: 2021-04-08 17:43:09,961 INFO: ------------------- PROTOCOL > FAILED (DONE 553/2953) > > Thanks in advance, > Matt > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Matt H. <ma...@ms...> - 2021-04-14 19:56:24
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We use Scipion 3 to read in 2000+ micrographs and process them with motioncor2. Scipion 3 seems to stop processing after anywhere from 10 - 500 movies. Error below. This worked fine under Scipion 2. We don't think we've made any changes to our workflow. Any ideas? 00309: 2021-04-08 17:43:08,289 INFO: STARTED: processMovieStep, step 561, time 2021-04-08 17:43:08.288900 00310: 2021-04-08 17:43:08,302 INFO: Processing movie: Runs/000790_ProtMotionCorr/tmp/movie_000560/dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11.tif 00311: 2021-04-08 17:43:08,304 INFO: /programs/x86_64-linux/scipion/3.0.0/software/em/motioncor2-1.3.2/bin/MotionCor2_1.3.2-Cuda101 -InTiff "dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11.tif" -OutMrc "../../extra/dbulkley_20210204_110kx_Apof_240-11_Feb05_10.50.11_aligned_mic.mrc" -Patch 7 5 -MaskCent 0 0 -MaskSize 1 1 -FtBin 2.0 -Tol 0.5 -Group 1 -FmDose 0.67 -Throw 1 -Trunc 0 -PixSize 0.1865 -kV 200.0 -LogFile ../../extra/micrograph_000560_ -InitDose 0.0 -OutStack 0 -Mag 1.000 1.000 0.000 -Gain "/msg/data6/scratch/Gain-Refs/K3-GainRefx1m3_20210405.mrc" -RotGain 0 -FlipGain 0 -Gpu 6 -SumRange 0.0 0.0 -InFmMotion 1 00312: 2021-04-08 17:43:09,961 INFO: ------------------- PROTOCOL FAILED (DONE 553/2953) Thanks in advance, Matt |
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From: Grigory S. <sha...@gm...> - 2021-04-14 14:23:52
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In this case I'd suggest optimizing the picking rather than waste computing resources on classifying out noise. 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 Wed, Apr 14, 2021 at 2:48 PM Carlos Oscar Sorzano <co...@cn...> wrote: > I am afraid he may be referring to particles in the ice. For getting rid > of these particles, you may find more useful the deep consensus algorithm > whose input is a couple of pickings. The eliminate empty classes is > currently used mostly for classes, and as there are not so many, it does > not take so long on a single processor. > > Cheers, Carlos Oscar > El 14/04/2021 a las 15:38, Grigory Sharov escribió: > > Hi Dmitry, > > I haven't used that protocol so can't comment on it. By empty particles do > you mean completely black particles with 0.0 or some particles with noise > inside? You could use relion_image_handler with the "--stats" option to > find the former ones. > > Getting rid of second ones is more difficult. > > 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear colleagues, >> >> >> One more question about effective deletion of the empty particles in the >> dataset. >> >> Correct me if I am wrong, but the dedicated tools for that purpose are: >> xmipp - eliminate empty classes // particles. >> >> I would like to ask if there is a possibility to boost the processing >> speed of them? I am afraid that it is using only 1 MPI and in case of few >> millions particles the processing on 1 MPI can take few days. >> >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> _______________________________________________ >> 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 > > |
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From: Grigory S. <sha...@gm...> - 2021-04-14 14:20:11
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Hi Dmitry, the sidesplitter plugin was made mostly for testing purposes (since it runs on a single iteration), so you can't use output half maps unless you run postprocess manually outside Scipion. The proper way to run it would be with relion plugin as described here: https://github.com/StructuralBiology-ICLMedicine/SIDESPLITTER/blob/master/sidesplitter_wrapper.sh 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > My question is about Sidesplitter- local filter. > > As an output we get 2 half-maps. > > My question is how to use them (the half-maps) as an input in the > relion-postprocessing protocol, since currently the previous refinement > protocol only is required? > > > Thank you! > > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos O. S. <co...@cn...> - 2021-04-14 13:48:38
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I am afraid he may be referring to particles in the ice. For getting rid of these particles, you may find more useful the deep consensus algorithm whose input is a couple of pickings. The eliminate empty classes is currently used mostly for classes, and as there are not so many, it does not take so long on a single processor. Cheers, Carlos Oscar El 14/04/2021 a las 15:38, Grigory Sharov escribió: > Hi Dmitry, > > I haven't used that protocol so can't comment on it. By empty > particles do you mean completely black particles with 0.0 or some > particles with noise inside? You could use relion_image_handler with > the "--stats" option to find the former ones. > > Getting rid of second ones is more difficult. > > 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm... > <mailto:Sem...@gm...>> wrote: > > Dear colleagues, > > > One more question about effective deletion of the empty particles > in the dataset. > > Correct me if I am wrong, but the dedicated tools for that purpose > are: xmipp - eliminate empty classes // particles. > > I would like to ask if there is a possibility to boost the > processing speed of them? I am afraid that it is using only 1 MPI > and in case of few millions particles the processing on 1 MPI can > take few days. > > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <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...> - 2021-04-14 13:39:17
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Hi Dmitry, I haven't used that protocol so can't comment on it. By empty particles do you mean completely black particles with 0.0 or some particles with noise inside? You could use relion_image_handler with the "--stats" option to find the former ones. Getting rid of second ones is more difficult. 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > > One more question about effective deletion of the empty particles in the > dataset. > > Correct me if I am wrong, but the dedicated tools for that purpose are: > xmipp - eliminate empty classes // particles. > > I would like to ask if there is a possibility to boost the processing > speed of them? I am afraid that it is using only 1 MPI and in case of few > millions particles the processing on 1 MPI can take few days. > > > Thank you > > Sincerely, > Dmitry > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-04-14 11:50:28
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Dear colleagues, My question is about Sidesplitter- local filter. As an output we get 2 half-maps. My question is how to use them (the half-maps) as an input in the relion-postprocessing protocol, since currently the previous refinement protocol only is required? Thank you! Sincerely, Dmitry |
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From: Dmitry S. <Sem...@gm...> - 2021-04-14 11:50:24
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Dear colleagues, One more question about effective deletion of the empty particles in the dataset. Correct me if I am wrong, but the dedicated tools for that purpose are: xmipp - eliminate empty classes // particles. I would like to ask if there is a possibility to boost the processing speed of them? I am afraid that it is using only 1 MPI and in case of few millions particles the processing on 1 MPI can take few days. Thank you Sincerely, Dmitry |
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From: Grigory S. <sha...@gm...> - 2021-04-13 10:18:05
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Hello Avi, could you attach the first 100 lines of the star files here so I can test it? 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, Apr 13, 2021 at 11:15 AM Bandyopadhyay, Abhishek <ba...@pu...> wrote: > Hello, > I am Avi, currently working at Purdue University. I am > using Scipion for the purpose of localized reconstruction. > > As I am importing my star file into Scipion using the import particles > job, unfortunately, the program changes the Angstrom/pixel value in the > .star file. > > For example, my original star file has an Ang/px value of 1.32. I then > started a Scipion Import Particles job. I defined all the parameters ( > voltage, spehrical abberation, mag, ang/px etc), but the Scipion Import > Particles program outputs the star file as having an Ang/px value of 1. > Unfortunately, there was no way for me to change this at the stage of > Define subparticles or Extract Subparticles. Both the Define Subparticles > and Extract Subparticles jobs considered the input star file having an > Ang/px value of 1, which is incorrect. > > I was wondering if you are aware of this issue and if so, could you kindly > suggest how to tackle this issue? > > I managed to overcome this problem by shifting to command line operations > for Relion reconstruct and then Relion 3DClassification. However, it would > really be helpful if this problem can be solved at the very beginning, > which is at the import particle step. > > Thank you very much for your help. > > Best regards, > > Avi > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-04-13 10:08:41
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Dear Pablo, Yes, I figured this out as well. So in case that the name of the micrographs does not match as 1 to 1 the coordinate transfer is not possible…. Sincerely, Dmitry > On 13. Apr 2021, at 11:56, Pablo Conesa <pc...@cn...> wrote: > > If I'm right, you need one coordinate star file to match the name of the micrograph. > > Also you need an existing setOfMics having the same name. > > Could you please, send an example of one coordinates file? > > > > On 12/4/21 22:01, Dmitry A. Semchonok wrote: >> Dear colleagues, >> >> I am sorry if this question perhaps was answered. It is still not all clear for me: >> how can I import the relion coordinate. star file into the scipion? >> I used the import coordinate option, but somehow, no coordinates were added. >> >> Thank you in advance. >> >> Sincerely, >> Dmitry >> >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- > Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es/> team > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> |
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From: Pablo C. <pc...@cn...> - 2021-04-13 10:06:14
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If I'm right, you need one coordinate star file to match the name of the micrograph. Also you need an existing setOfMics having the same name. Could you please, send an example of one coordinates file? On 12/4/21 22:01, Dmitry A. Semchonok wrote: > > Dear colleagues, > > I am sorry if this question perhaps was answered. It is still not all > clear for me: > > how can I import the relion coordinate. star file into the scipion? > > I used the import coordinate option, but somehow, no coordinates were > added. > > Thank you in advance. > > Sincerely, > > Dmitry > > > > _______________________________________________ > 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: Bandyopadhyay, A. <ba...@pu...> - 2021-04-12 23:09:07
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Hello,
I am Avi, currently working at Purdue University. I am using Scipion for the purpose of localized reconstruction.
As I am importing my star file into Scipion using the import particles job, unfortunately, the program changes the Angstrom/pixel value in the .star file.
For example, my original star file has an Ang/px value of 1.32. I then started a Scipion Import Particles job. I defined all the parameters ( voltage, spehrical abberation, mag, ang/px etc), but the Scipion Import Particles program outputs the star file as having an Ang/px value of 1. Unfortunately, there was no way for me to change this at the stage of Define subparticles or Extract Subparticles. Both the Define Subparticles and Extract Subparticles jobs considered the input star file having an Ang/px value of 1, which is incorrect.
I was wondering if you are aware of this issue and if so, could you kindly suggest how to tackle this issue?
I managed to overcome this problem by shifting to command line operations for Relion reconstruct and then Relion 3DClassification. However, it would really be helpful if this problem can be solved at the very beginning, which is at the import particle step.
Thank you very much for your help.
Best regards,
Avi
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