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From: <pc...@cn...> - 2020-12-27 14:40:43
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<div dir='auto'><div dir="auto">We recently saw cryosparc not responding to our request. We weren't defining a timeout so the consequence is that, a project never opens and freezes.<div dir="auto"><br></div><div dir="auto">A restart of cryosparc fixed it. Additionally we are working, if not released yet (Yunior should know), on a tolerance fix to avoid the freeze even if cs does not respond.</div></div><div><br><div class="elided-text">El 27 dic. 2020 11:56, Grigory Sharov <sha...@gm...> escribió:<br type="attribution"><blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto"><div>Hi Dmitry,<div dir="auto"><br></div><div dir="auto">So you have a project with few cryosparc protocols and nothing running there. </div><div dir="auto">Do you mean that the project window takes a lot of time to open? What's the total number of protocols? Could you maybe share the whole project workflow (export it to json) privately? </div><div dir="auto"><br></div><div dir="auto">We did start working on profiling scipion performance so this will be a useful case </div><div dir="auto"><br></div><div dir="auto">Thanks, </div><div dir="auto">Grigory </div><br><br><div class="elided-text"><div dir="ltr">On Tue, Dec 22, 2020, 09:20 Dmitry Semchonok <<a href="mailto:Sem...@gm...">Sem...@gm...</a>> wrote:<br></div><blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex">Dear colleagues,<br> <br> We have a slowing down of any of our projects that contains any of cryoSPARC protocol inside the SCIPION even when no active process is running. <br> (I do not mean the conversion step).<br> <br> <br> At the same time, running the same task separately on the cryoSPARC server only does not give any delay in response and finished much faster.<br> <br> <br> Do you perhaps know the reason and the possible fix?<br> <br> <br> Thank you!<br> <br> Sincerely,<br> Dmitry<br> <br> <br> <br> <br> <br> <br> <br> _______________________________________________<br> scipion-users mailing list<br> <a href="mailto:sci...@li...">sci...@li...</a><br> <a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br> </blockquote></div></div></div> </blockquote></div><br></div></div> |
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From: Grigory S. <sha...@gm...> - 2020-12-27 10:57:09
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Hi Dmitry, So you have a project with few cryosparc protocols and nothing running there. Do you mean that the project window takes a lot of time to open? What's the total number of protocols? Could you maybe share the whole project workflow (export it to json) privately? We did start working on profiling scipion performance so this will be a useful case Thanks, Grigory On Tue, Dec 22, 2020, 09:20 Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > We have a slowing down of any of our projects that contains any of > cryoSPARC protocol inside the SCIPION even when no active process is > running. > (I do not mean the conversion step). > > > At the same time, running the same task separately on the cryoSPARC server > only does not give any delay in response and finished much faster. > > > Do you perhaps know the reason and the possible fix? > > > Thank you! > > Sincerely, > Dmitry > > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Moustafa, I. M. <ri...@ps...> - 2020-12-25 17:06:05
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Thank you Grigory for the fix. It works now! Ibrahim ________________________________ From: Grigory Sharov <sha...@gm...> Sent: Friday, December 25, 2020 8:10 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import relion particles error Hi, I have reproduced the problem and just released a hotfix. To update, run scipion3 installp -p scipion-em-relion --noBin This will install the 3.0.0b8 plugin with the fix for you. Thanks a lot for reporting this issue! 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, Dec 25, 2020 at 5:31 AM Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> wrote: Hello Grigory, 1) The plugin used is scipion-em-relion 3.0.0b2 2) Yes, particles imported from a _data.star file 3) Attached is a truncated version of run_data.star file with the first 100 lines Thanks for help. Ibrahim ________________________________ From: Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> Sent: Thursday, December 24, 2020 5:58 AM To: Mailing list for Scipion users <sci...@li...<mailto:sci...@li...>> Subject: Re: [scipion-users] Import relion particles error Hello Ibrahim, could you please provide the following information so I could investigate further: 1) what relion plugin version do you use? (scipion3 installp -h) 2) do you import particles from a _data star file? 3) could you print here the first 100 lines of this star file? Thanks! 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, Dec 24, 2020 at 7:45 AM Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> wrote: Dear all, I am trying to import particles from relion.3.1.622 in Scipion v3.0.4 but I get the following error: Protocol failed: 'Row' object has no attribute 'rlnCtfMaxResolution' Not sure why convert31.py is not able to import the particles, insisting to read an attribute that does not exist in the star file. Any suggestion will be appreciated. Thank you, Ibrahim _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8dc626cb6e3141c5302d08d8a8d6916f%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637444986811347213%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4BOb3%2BlvK6YxjwBwSC%2BQf8q5mYrXosWWCEr9QpmPXWc%3D&reserved=0> _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8dc626cb6e3141c5302d08d8a8d6916f%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637444986811347213%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4BOb3%2BlvK6YxjwBwSC%2BQf8q5mYrXosWWCEr9QpmPXWc%3D&reserved=0> |
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From: Grigory S. <sha...@gm...> - 2020-12-25 13:11:04
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Hi, I have reproduced the problem and just released a hotfix. To update, run *scipion3 installp -p scipion-em-relion --noBin* This will install the 3.0.0b8 plugin with the fix for you. Thanks a lot for reporting this issue! 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, Dec 25, 2020 at 5:31 AM Moustafa, Ibrahim M. <ri...@ps...> wrote: > Hello Grigory, > > 1) The plugin used is scipion-em-relion 3.0.0b2 > > 2) Yes, particles imported from a _data.star file > > 3) Attached is a truncated version of run_data.star file with the first > 100 lines > > > Thanks for help. > > Ibrahim > > ------------------------------ > *From:* Grigory Sharov <sha...@gm...> > *Sent:* Thursday, December 24, 2020 5:58 AM > *To:* Mailing list for Scipion users <sci...@li...> > *Subject:* Re: [scipion-users] Import relion particles error > > Hello Ibrahim, > > could you please provide the following information so I could investigate > further: > > 1) what relion plugin version do you use? (scipion3 installp -h) > 2) do you import particles from a _data star file? > 3) could you print here the first 100 lines of this star file? > > Thanks! > > 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, Dec 24, 2020 at 7:45 AM Moustafa, Ibrahim M. <ri...@ps...> wrote: > > Dear all, > > I am trying to import particles from relion.3.1.622 in Scipion v3.0.4 > but I get the following error: > > Protocol failed: 'Row' object has no attribute 'rlnCtfMaxResolution' > > Not sure why convert31.py is not able to import the particles, insisting > to read an attribute that does not exist in the star file. > > Any suggestion will be appreciated. > > Thank you, > Ibrahim > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7Ca622cf49455d4d4d21df08d8a7faf54a%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637444043609394645%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=A3QvALsCnXCCfWeeYFt1aEq6t3Jadghuy04ukazXUqI%3D&reserved=0> > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Moustafa, I. M. <ri...@ps...> - 2020-12-25 05:31:22
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Hello Grigory, 1) The plugin used is scipion-em-relion 3.0.0b2 2) Yes, particles imported from a _data.star file 3) Attached is a truncated version of run_data.star file with the first 100 lines Thanks for help. Ibrahim ________________________________ From: Grigory Sharov <sha...@gm...> Sent: Thursday, December 24, 2020 5:58 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] Import relion particles error Hello Ibrahim, could you please provide the following information so I could investigate further: 1) what relion plugin version do you use? (scipion3 installp -h) 2) do you import particles from a _data star file? 3) could you print here the first 100 lines of this star file? Thanks! 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, Dec 24, 2020 at 7:45 AM Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> wrote: Dear all, I am trying to import particles from relion.3.1.622 in Scipion v3.0.4 but I get the following error: Protocol failed: 'Row' object has no attribute 'rlnCtfMaxResolution' Not sure why convert31.py is not able to import the particles, insisting to read an attribute that does not exist in the star file. Any suggestion will be appreciated. Thank you, Ibrahim _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7Ca622cf49455d4d4d21df08d8a7faf54a%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637444043609394645%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=A3QvALsCnXCCfWeeYFt1aEq6t3Jadghuy04ukazXUqI%3D&reserved=0> |
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From: Grigory S. <sha...@gm...> - 2020-12-24 10:59:00
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Hello Ibrahim, could you please provide the following information so I could investigate further: 1) what relion plugin version do you use? (scipion3 installp -h) 2) do you import particles from a _data star file? 3) could you print here the first 100 lines of this star file? Thanks! 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, Dec 24, 2020 at 7:45 AM Moustafa, Ibrahim M. <ri...@ps...> wrote: > Dear all, > > I am trying to import particles from relion.3.1.622 in Scipion v3.0.4 > but I get the following error: > > Protocol failed: 'Row' object has no attribute 'rlnCtfMaxResolution' > > Not sure why convert31.py is not able to import the particles, insisting > to read an attribute that does not exist in the star file. > > Any suggestion will be appreciated. > > Thank you, > Ibrahim > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Moustafa, I. M. <ri...@ps...> - 2020-12-24 07:45:10
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Dear all, I am trying to import particles from relion.3.1.622 in Scipion v3.0.4 but I get the following error: Protocol failed: 'Row' object has no attribute 'rlnCtfMaxResolution' Not sure why convert31.py is not able to import the particles, insisting to read an attribute that does not exist in the star file. Any suggestion will be appreciated. Thank you, Ibrahim |
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From: David M. <dma...@ub...> - 2020-12-23 11:26:12
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Hi Ane-Pascale, Probably you never got my mail due to a misconfiguration on my mail server. My apologies. To be honest, I can't recognize this error. The only thing that rings the bell is the last message 《Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists》 which is totally weird. Can you post here the returning message for the next commands: 'scipion3 python -m pip list', 'scipion3 installp --help' and 'scipion3 installb'. Thanks and sorry for the inconveniences.. <http://ucm.es/> _____ Dr. David Maluenda Niubó dma...@ub...<mailto:dma...@ub...> - (+34) 619 029 310 Wavefront Engineering Group<https://webgrec.ub.edu/cgi-bin/3DADREC/crfitgrup.cgi?PAR=GRENFONA> Applied Physics - UB<https://www.ub.edu/portal/web/dp-fisica-aplicada> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Tue, Dec 8, 2020 at 5:15 PM David Maluenda <dma...@cn...<mailto:dma...@cn...>> wrote: Hi Ane-Pascale, To be honest, I can't recognize this error. The only thing that rings the bell is the last message 《Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists》 which is totally weird. Can you post here the returning message for the next commands: 'scipion3 python -m pip list', 'scipion3 installp --help' and 'scipion3 installb'. Thanks and sorry for the inconveniences.. _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub...<mailto:dma...@ub...> Wavefront Engineering Group Applied Physics (UB) El lun., 7 dic. 2020 10:23, Anne-Pascale JAUDIER <ann...@i2...<mailto:ann...@i2...>> escribió: Hi Gregory, Effectively Ihave installed it from the command line without error. Thanks a lot, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 ________________________________ De: "Grigory Sharov" <sha...@gm...<mailto:sha...@gm...>> À: "scipion-users" <sci...@li...<mailto:sci...@li...>> Envoyé: Samedi 5 Décembre 2020 14:32:44 Objet: Re: [scipion-users] error installing deepLearningToolkitUtils Hi Anne-Pascale, I'm not familiar with either xmipp or plugin manager code but have you tried "scipion installb deepLearningToolkit" from the command line? It will take about 20 min to install though.. 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, Dec 4, 2020 at 9:13 AM Anne-Pascale JAUDIER <ann...@i2...<mailto:ann...@i2...>> wrote: Hi, I have an error during the installation of the pluggin deepLearningToolkitUtils. The error is : ------------------------------------ /bin/sh: 1: update: not found 00002: Exception in thread plugin-manager: 00003: Traceback (most recent call last): 00004: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 932, in _bootstrap_inner 00005: self.run() 00006: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/threading.py", line 870, in run 00007: self._target(*self._args, **self._kwargs) 00008: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 740, in _applyOperations 00009: self.reloadInstalledPlugin(op.getObjParent()) 00010: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 898, in reloadInstalledPlugin 00011: self.tree.insert(pluginName, "end", 00012: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_manager.py", line 103, in insert 00013: ttk.Treeview.insert(self, parent, index, iid, **kw) 00014: File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/ttk.py", line 1366, in insert 00015: res = self.tk.call(self._w, "insert", parent, index, 00016: _tkinter.TclError: Item deepLearningToolkit-0.2[scipion-em-xmipp] already exists ----------------------------- Thanks, Anne-Pascale ---------------------------------------------------------------------- Anne-Pascale Jaudier SICS – I2BC Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette 01 69 82 34 74 _______________________________________________ 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 Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account. |
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From: Dmitry S. <Sem...@gm...> - 2020-12-22 09:20:16
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Dear colleagues, We have a slowing down of any of our projects that contains any of cryoSPARC protocol inside the SCIPION even when no active process is running. (I do not mean the conversion step). At the same time, running the same task separately on the cryoSPARC server only does not give any delay in response and finished much faster. Do you perhaps know the reason and the possible fix? Thank you! Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2020-12-15 12:50:21
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Thanks Dmitry, I've fixed the link but will take some time until documentation is built again. Please find it here in the meantime: https://scipion-em.github.io/docs/docs/images/Conventions/Symmetry/axis.bild On 15/12/20 13:24, Dmitry Semchonok wrote: > Dear colleagues, > > On the SCIPION3 website page there is a great example of the different > types of symmetry: > > https://scipion-em.github.io/docs/docs/developer/symmetries > > But the PDB links of those symmetry models examples are not working. > > > Could you please fix the links? > > Or advice those PDB’s? > > > 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: Dmitry S. <Sem...@gm...> - 2020-12-15 12:24:56
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Dear colleagues, On the SCIPION3 website page there is a great example of the different types of symmetry: https://scipion-em.github.io/docs/docs/developer/symmetries <https://scipion-em.github.io/docs/docs/developer/symmetries> But the PDB links of those symmetry models examples are not working. Could you please fix the links? Or advice those PDB’s? Thank you in advance. Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2020-12-15 08:33:46
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When this happens: WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH Conda related installations are probably not going to work. Set the CONDA_ACTIVATION_CMD variable in scipion.conf file. Here you can find some detailed descritpion: https://github.com/scipion-em/scipion-em-sphire#plugin-integration On 14/12/20 16:08, Dmitry Semchonok wrote: > P.s. > > And this is the error ( bit different) on the other PC: > > > $ scipion3 installb deepLearningToolkit > Scipion v3.0.7 - Eugenius > WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not > defined. Relying on conda being in the PATH > Error retrieving plugin relion binaries: CUDA_LIB (or > RELION_CUDA_LIB) is defined, but not CUDA_BIN (or RELION_CUDA_BIN), > please execute scipion config --update > WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not > defined. Relying on conda being in the PATH > WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not > defined. Relying on conda being in the PATH > WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not > defined. Relying on conda being in the PATH > Building deepLearningToolkit-0.2 ... > Skipping command: wget -nv -c -O > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz > mv -v > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part > /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz > All targets exist. > Skipping command: tar -xf deepLearningToolkit.tgz > All targets exist. > Skipping command: if ls > /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. > Driver version: 450' ; else echo ; echo ' > Xmipp installation not > found, please install it first (xmippSrc or xmippBin*).';echo; fi > All targets exist. > cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit > export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash > hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 > pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 > scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && > pip install numpy==1.18.4 numpy==1.18.4 && conda env export > > xmipp_DLTK_v0.3.yml > > CondaValueError: prefix already exists: > /home/user/.conda/envs/xmipp_DLTK_v0.3 > > Traceback (most recent call last): > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 457, in <module> > main() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", > line 297, in main > installPluginMethods() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 259, in installPluginMethods > pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmipp_DLTK_v0.3.yml' > not built (after running 'export PYTHONPATH="" && eval > "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create > --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 > scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 > scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && > pip install numpy==1.18.4 numpy==1.18.4 && conda env export > > xmipp_DLTK_v0.3.yml') > Error at main: target > '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmipp_DLTK_v0.3.yml' > not built (after running 'export PYTHONPATH="" && eval > "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create > --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 > scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 > scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && > pip install numpy==1.18.4 numpy==1.18.4 && conda env export > > xmipp_DLTK_v0.3.yml') > > > > > > > > > >> On 14. Dec 2020, at 16:04, Dmitry Semchonok <sem...@gm... >> <mailto:sem...@gm...>> wrote: >> >> Dear colleagues, >> >> We are experiencing some issue with the installation of the >> deepLearning toolkit. >> >> >> While installing from the command line we have the following error: >> >> >> export PYTHONPATH="" && eval "$(/usr/local/EMAN_2.21/bin/conda >> shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 >> python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 >> keras=2.2 scikit-learn=0.22 -c anaconda && conda activate >> xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda >> env export > xmipp_DLTK_v0.3.yml >> usage: conda [-h] [-V] command ... >> conda: error: argument command: invalid choice: >> u'/usr/local/EMAN_2.21/bin/conda' (choose from u'info', u'help', >> u'list', u'search', u'create', u'install', u'update', u'upgrade', >> u'remove', u'uninstall', u'config', u'clean', u'package') >> >> CondaValueError: prefix already exists: >> /home/panos/.conda/envs/xmipp_DLTK_v0.3 >> >> >> Could you please advice how to solve that ? >> >> >> Thank you >> >> >> 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: Pablo C. <pc...@cn...> - 2020-12-15 08:28:56
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Hi Dmitry, you are using conda provided by eman 2.21 We have not tested that at all and in some cases we've seen issues related to the MPI library provided eman. I'd avoid this: eval "$(/usr/local/EMAN_2.21/bin/conda shell.bash hook)" This is probably coming from a variable in the scipion.conf named CONDA_ACTIVATION_CMD Please set it to point to a non eman conda path (Miniconda installation or anaconda) On 14/12/20 16:04, Dmitry Semchonok wrote: > Dear colleagues, > > We are experiencing some issue with the installation of the > deepLearning toolkit. > > > While installing from the command line we have the following error: > > > export PYTHONPATH="" && eval "$(/usr/local/EMAN_2.21/bin/conda > shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 > python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 > keras=2.2 scikit-learn=0.22 -c anaconda && conda activate > xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda > env export > xmipp_DLTK_v0.3.yml > usage: conda [-h] [-V] command ... > conda: error: argument command: invalid choice: > u'/usr/local/EMAN_2.21/bin/conda' (choose from u'info', u'help', > u'list', u'search', u'create', u'install', u'update', u'upgrade', > u'remove', u'uninstall', u'config', u'clean', u'package') > > CondaValueError: prefix already exists: > /home/panos/.conda/envs/xmipp_DLTK_v0.3 > > > Could you please advice how to solve that ? > > > Thank you > > > 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: Dmitry S. <Sem...@gm...> - 2020-12-14 15:08:46
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P.s. And this is the error ( bit different) on the other PC: $ scipion3 installb deepLearningToolkit Scipion v3.0.7 - Eugenius WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH Error retrieving plugin relion binaries: CUDA_LIB (or RELION_CUDA_LIB) is defined, but not CUDA_BIN (or RELION_CUDA_BIN), please execute scipion config --update WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH WARNING!!_condaActivationCmd: CONDA_ACTIVATION_CMD variable not defined. Relying on conda being in the PATH Building deepLearningToolkit-0.2 ... Skipping command: wget -nv -c -O /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz <http://scipion.cnb.csic.es/downloads/scipion/software/external/deepLearningToolkit.tgz> mv -v /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz.part /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit.tgz All targets exist. Skipping command: tar -xf deepLearningToolkit.tgz All targets exist. Skipping command: if ls /home/user/Data/Software/Scipion3/software/em/xmipp/lib/libXmipp.so > /dev/null ; then touch xmippLibToken; echo ' > CUDA support find. Driver version: 450' ; else echo ; echo ' > Xmipp installation not found, please install it first (xmippSrc or xmippBin*).';echo; fi All targets exist. cd /home/user/Data/Software/Scipion3/software/em/deepLearningToolkit export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml CondaValueError: prefix already exists: /home/user/.conda/envs/xmipp_DLTK_v0.3 Traceback (most recent call last): File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 457, in <module> main() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/__main__.py", line 297, in main installPluginMethods() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 259, in installPluginMethods pinfo.installBin({'args': [binTarget, '-j', numberProcessor]}) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmipp_DLTK_v0.3.yml' not built (after running 'export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml') Error at main: target '/home/user/Data/Software/Scipion3/software/em/deepLearningToolkit/xmipp_DLTK_v0.3.yml' not built (after running 'export PYTHONPATH="" && eval "$(/usr/local/EMAN2/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml') > On 14. Dec 2020, at 16:04, Dmitry Semchonok <sem...@gm...> wrote: > > Dear colleagues, > > We are experiencing some issue with the installation of the deepLearning toolkit. > > > While installing from the command line we have the following error: > > > export PYTHONPATH="" && eval "$(/usr/local/EMAN_2.21/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml > usage: conda [-h] [-V] command ... > conda: error: argument command: invalid choice: u'/usr/local/EMAN_2.21/bin/conda' (choose from u'info', u'help', u'list', u'search', u'create', u'install', u'update', u'upgrade', u'remove', u'uninstall', u'config', u'clean', u'package') > > CondaValueError: prefix already exists: /home/panos/.conda/envs/xmipp_DLTK_v0.3 > > > Could you please advice how to solve that ? > > > Thank you > > > Sincerely, > Dmitry > |
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From: Dmitry S. <Sem...@gm...> - 2020-12-14 15:04:32
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Dear colleagues, We are experiencing some issue with the installation of the deepLearning toolkit. While installing from the command line we have the following error: export PYTHONPATH="" && eval "$(/usr/local/EMAN_2.21/bin/conda shell.bash hook)" && conda create --force --yes -n xmipp_DLTK_v0.3 python=3 pandas=0.23 scikit-image=0.14 opencv=3.4 tensorflow-gpu=1.15 keras=2.2 scikit-learn=0.22 -c anaconda && conda activate xmipp_DLTK_v0.3 && pip install numpy==1.18.4 numpy==1.18.4 && conda env export > xmipp_DLTK_v0.3.yml usage: conda [-h] [-V] command ... conda: error: argument command: invalid choice: u'/usr/local/EMAN_2.21/bin/conda' (choose from u'info', u'help', u'list', u'search', u'create', u'install', u'update', u'upgrade', u'remove', u'uninstall', u'config', u'clean', u'package') CondaValueError: prefix already exists: /home/panos/.conda/envs/xmipp_DLTK_v0.3 Could you please advice how to solve that ? Thank you Sincerely, Dmitry |
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From: Eng. A. <ala...@gm...> - 2020-12-12 17:27:05
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Hi,
Thanks in advance, recently I was using scipion and it does work
perfectly. I got some issues while I tried to install RELION it keeps
saying FAILED, any suggestions please ?
I did follow the installation using ubuntu with conda
Thanks,
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From: Dmitry S. <Sem...@gm...> - 2020-12-10 15:15:05
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Dear Grigory, Yes indeed it worked. Thank you! I still would like to understand why the recommended settings that are described in the Help for te protocol run: ProtRelionCreateMask do not work? As you see in this Help the 15-20 angstrom lowpass filter may work as well. Please see my test image below. Sincerely, Dmitry > On 10. Dec 2020, at 14:39, Grigory Sharov <sha...@gm...> wrote: > > Hi, > > I've checked this and as I said before your comparison is wrong. Set in relion lowpass to -1, extend and soft edge to 0 and then the same threshold as in xmipp will give you (almost) the same volume. > > 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, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > I guess it happens not often, but I noticed that happening more ofter after the bayesian polishing. > > The log shows the same values as I set in. > > Please let me know in case you want see the problem on our server directly (if it can help somehow). > > > Sincerely, > Dmitry > > > > >> On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> I'll check this, thanks >> >> On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> Dear Carlos Oscar and Grigory, >> >> Thank you for your answers. >> >> The following image illustrates the problem. >> >> 1. Thank you Carlos Oscar — on the image below I compared the Xmipp masking and is works as it should based on the correct threshold. >> 2. Thank you Grigory — no the binning value seems to be ok. >> >> >> Sincerely, >> Dmitry >> >> >> >> >> >> >> >> >> >> >> >> >> >>> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >>> >>> Hi, >>> >>> You can check the output log for the protocol to see the executed relion command. I think you have lowpass filtering enabled so the threshold you choose must be selected on a filtered volume. >>> >>> On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> Dear colleagues, >>> >>> >>> It may be the bug of issue happening after the particle polishing with the relion masking 3D protocol. >>> >>> >>> It seems that it has a 10x times issue. >>> >>> So, adjusting the volume threshold in chimera (for 3D mask protocol and then postprocessing) till no extra noise is appeared we get the value for ex. 0.00658. But if you then put this value to the relion 3D mask protocol you get completely dark images. At the same time if you set the threshold value 0.000658 you get the fine mask. >>> >>> >>> I am not sure what causes that but I noticed that behaviour happening sometimes after the execution of the Bayesian polishing. >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> P.s. it will be great to have unbiased protocol for masking >>> >>> Or is there any exist already? >>> >>> _______________________________________________ >>> 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> >> >> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at 11.40.39.png> > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2020-12-10 14:53:26
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Hi Dmitry, I cannot tell, but it would seem as if the refinement FSC is masked beyond a given frequency while the postprocessing is not. Kind regards, Carlos Oscar El 10/12/2020 a las 15:11, Dmitry Semchonok escribió: > Dear colleagues, > > Another small question — > > Why, at your opinion, the relion 3D refinement (after the bayesian > polishing) finishes fine but the postprocessing file have a FSC curve > that does not reach “0” value? > > Thank you! > > Sincerely, > Dmitry > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-12-10 14:28:32
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Hi, lowpass 15A requires a different threshold than low pass -1. PS. Please do not attach images bigger than 400Kb. 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, Dec 10, 2020 at 2:19 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > Yes indeed it worked. > Thank you! > > I still would like to understand why the recommended settings that are > described in the Help for te protocol run: ProtRelionCreateMask do not work? > As you see in this Help the 15-20 angstrom lowpass filter may work as > well. > > Please see my test image below. > > Sincerely, > Dmitry > > > > > > > On 10. Dec 2020, at 14:39, Grigory Sharov <sha...@gm...> > wrote: > > Hi, > > I've checked this and as I said before your comparison is wrong. Set in > relion lowpass to -1, extend and soft edge to 0 and then the same threshold > as in xmipp will give you (almost) the same volume. > > 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, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm...> > wrote: > >> I guess it happens not often, but I noticed that happening more ofter >> after the bayesian polishing. >> >> The log shows the same values as I set in. >> >> Please let me know in case you want see the problem on our server >> directly (if it can help somehow). >> >> >> Sincerely, >> Dmitry >> >> >> >> >> On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm...> >> wrote: >> >> I'll check this, thanks >> >> On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm...> wrote: >> >>> Dear Carlos Oscar and Grigory, >>> >>> Thank you for your answers. >>> >>> The following image illustrates the problem. >>> >>> 1. Thank you Carlos Oscar — on the image below I compared the Xmipp >>> masking and is works as it should based on the correct threshold. >>> 2. Thank you Grigory — no the binning value seems to be ok. >>> >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> >>> wrote: >>> >>> Hi, >>> >>> You can check the output log for the protocol to see the executed relion >>> command. I think you have lowpass filtering enabled so the threshold you >>> choose must be selected on a filtered volume. >>> >>> On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> >>> wrote: >>> >>>> Dear colleagues, >>>> >>>> >>>> It may be the bug of issue happening after the particle polishing with >>>> the relion masking 3D protocol. >>>> >>>> >>>> It seems that it has a 10x times issue. >>>> >>>> So, adjusting the volume threshold in chimera (for 3D mask protocol and >>>> then postprocessing) till no extra noise is appeared we get the value for >>>> ex. 0.00658. But if you then put this value to the relion 3D mask protocol >>>> you get completely dark images. At the same time if you set the threshold >>>> value 0.000658 you get the fine mask. >>>> >>>> >>>> I am not sure what causes that but I noticed that behaviour happening >>>> sometimes after the execution of the Bayesian polishing. >>>> >>>> >>>> Sincerely, >>>> >>>> Dmitry >>>> >>>> >>>> P.s. it will be great to have unbiased protocol for masking >>>> Or is there any exist already? >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at >> 11.40.39.png> >> >> >> _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > |
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From: Grigory S. <sha...@gm...> - 2020-12-10 14:25:14
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Hi, lowpass 15A requires a different threshold than low pass -1. 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, Dec 10, 2020 at 2:19 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > Yes indeed it worked. > Thank you! > > I still would like to understand why the recommended settings that are > described in the Help for te protocol run: ProtRelionCreateMask do not work? > As you see in this Help the 15-20 angstrom lowpass filter may work as > well. > > Please see my test image below. > > Sincerely, > Dmitry > > > > > > On 10. Dec 2020, at 14:39, Grigory Sharov <sha...@gm...> > wrote: > > Hi, > > I've checked this and as I said before your comparison is wrong. Set in > relion lowpass to -1, extend and soft edge to 0 and then the same threshold > as in xmipp will give you (almost) the same volume. > > 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, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm...> > wrote: > >> I guess it happens not often, but I noticed that happening more ofter >> after the bayesian polishing. >> >> The log shows the same values as I set in. >> >> Please let me know in case you want see the problem on our server >> directly (if it can help somehow). >> >> >> Sincerely, >> Dmitry >> >> >> >> >> On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm...> >> wrote: >> >> I'll check this, thanks >> >> On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm...> wrote: >> >>> Dear Carlos Oscar and Grigory, >>> >>> Thank you for your answers. >>> >>> The following image illustrates the problem. >>> >>> 1. Thank you Carlos Oscar — on the image below I compared the Xmipp >>> masking and is works as it should based on the correct threshold. >>> 2. Thank you Grigory — no the binning value seems to be ok. >>> >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> >>> wrote: >>> >>> Hi, >>> >>> You can check the output log for the protocol to see the executed relion >>> command. I think you have lowpass filtering enabled so the threshold you >>> choose must be selected on a filtered volume. >>> >>> On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> >>> wrote: >>> >>>> Dear colleagues, >>>> >>>> >>>> It may be the bug of issue happening after the particle polishing with >>>> the relion masking 3D protocol. >>>> >>>> >>>> It seems that it has a 10x times issue. >>>> >>>> So, adjusting the volume threshold in chimera (for 3D mask protocol and >>>> then postprocessing) till no extra noise is appeared we get the value for >>>> ex. 0.00658. But if you then put this value to the relion 3D mask protocol >>>> you get completely dark images. At the same time if you set the threshold >>>> value 0.000658 you get the fine mask. >>>> >>>> >>>> I am not sure what causes that but I noticed that behaviour happening >>>> sometimes after the execution of the Bayesian polishing. >>>> >>>> >>>> Sincerely, >>>> >>>> Dmitry >>>> >>>> >>>> P.s. it will be great to have unbiased protocol for masking >>>> Or is there any exist already? >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at >> 11.40.39.png> >> >> >> _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > |
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From: Dmitry S. <Sem...@gm...> - 2020-12-10 14:12:02
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Dear colleagues, Another small question — Why, at your opinion, the relion 3D refinement (after the bayesian polishing) finishes fine but the postprocessing file have a FSC curve that does not reach “0” value? Thank you! Sincerely, Dmitry |
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From: Grigory S. <sha...@gm...> - 2020-12-10 13:39:48
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Hi, I've checked this and as I said before your comparison is wrong. Set in relion lowpass to -1, extend and soft edge to 0 and then the same threshold as in xmipp will give you (almost) the same volume. 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, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm...> wrote: > I guess it happens not often, but I noticed that happening more ofter > after the bayesian polishing. > > The log shows the same values as I set in. > > Please let me know in case you want see the problem on our server directly > (if it can help somehow). > > > Sincerely, > Dmitry > > > > > On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm...> > wrote: > > I'll check this, thanks > > On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm...> wrote: > >> Dear Carlos Oscar and Grigory, >> >> Thank you for your answers. >> >> The following image illustrates the problem. >> >> 1. Thank you Carlos Oscar — on the image below I compared the Xmipp >> masking and is works as it should based on the correct threshold. >> 2. Thank you Grigory — no the binning value seems to be ok. >> >> >> Sincerely, >> Dmitry >> >> >> >> >> >> >> >> >> >> >> >> >> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> >> wrote: >> >> Hi, >> >> You can check the output log for the protocol to see the executed relion >> command. I think you have lowpass filtering enabled so the threshold you >> choose must be selected on a filtered volume. >> >> On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> wrote: >> >>> Dear colleagues, >>> >>> >>> It may be the bug of issue happening after the particle polishing with >>> the relion masking 3D protocol. >>> >>> >>> It seems that it has a 10x times issue. >>> >>> So, adjusting the volume threshold in chimera (for 3D mask protocol and >>> then postprocessing) till no extra noise is appeared we get the value for >>> ex. 0.00658. But if you then put this value to the relion 3D mask protocol >>> you get completely dark images. At the same time if you set the threshold >>> value 0.000658 you get the fine mask. >>> >>> >>> I am not sure what causes that but I noticed that behaviour happening >>> sometimes after the execution of the Bayesian polishing. >>> >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> P.s. it will be great to have unbiased protocol for masking >>> Or is there any exist already? >>> >>> _______________________________________________ >>> 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 >> >> >> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at > 11.40.39.png> > > > |
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From: Dmitry S. <Sem...@gm...> - 2020-12-10 10:49:10
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Dear Carlos Oscar and Grigory, Thank you for your answers. The following image illustrates the problem. 1. Thank you Carlos Oscar — on the image below I compared the Xmipp masking and is works as it should based on the correct threshold. 2. Thank you Grigory — no the binning value seems to be ok. Sincerely, Dmitry > On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> wrote: > > Hi, > > You can check the output log for the protocol to see the executed relion command. I think you have lowpass filtering enabled so the threshold you choose must be selected on a filtered volume. > > On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear colleagues, > > > It may be the bug of issue happening after the particle polishing with the relion masking 3D protocol. > > > It seems that it has a 10x times issue. > > So, adjusting the volume threshold in chimera (for 3D mask protocol and then postprocessing) till no extra noise is appeared we get the value for ex. 0.00658. But if you then put this value to the relion 3D mask protocol you get completely dark images. At the same time if you set the threshold value 0.000658 you get the fine mask. > > > I am not sure what causes that but I noticed that behaviour happening sometimes after the execution of the Bayesian polishing. > > > Sincerely, > > Dmitry > > > > P.s. it will be great to have unbiased protocol for masking > > Or is there any exist already? > > _______________________________________________ > 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...> - 2020-12-10 10:32:55
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Hi, You can check the output log for the protocol to see the executed relion command. I think you have lowpass filtering enabled so the threshold you choose must be selected on a filtered volume. On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> wrote: > Dear colleagues, > > > > It may be the bug of issue happening after the particle polishing with the > relion masking 3D protocol. > > > > It seems that it has a 10x times issue. > > So, adjusting the volume threshold in chimera (for 3D mask protocol and > then postprocessing) till no extra noise is appeared we get the value for > ex. 0.00658. But if you then put this value to the relion 3D mask protocol > you get completely dark images. At the same time if you set the threshold > value 0.000658 you get the fine mask. > > > > I am not sure what causes that but I noticed that behaviour happening > sometimes after the execution of the Bayesian polishing. > > > > Sincerely, > > Dmitry > > > P.s. it will be great to have unbiased protocol for masking > Or is there any exist already? > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos O. S. <co...@cn...> - 2020-12-10 10:25:38
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Dear Dmitry, different operations may scale the grey values differently as the specific grey value is somewhat arbitrary. You may find useful the option of the xmipp create mask 3D protocol in which you specify a molecular mass and the threshold that defines an isosurface that encloses that molecular mass is selected. Cheers, Carlos Oscar El 10/12/2020 a las 9:46, Dmitry Semchonok escribió: > > Dear colleagues, > > It may be the bug of issue happening after the particle polishing with > the relion masking 3D protocol. > > It seems that it has a 10x times issue. > > So, adjusting the volume threshold in chimera (for 3D mask protocol > and then postprocessing) till no extra noise is appeared we get the > value for ex. 0.00658. But if you then put this value to the relion 3D > mask protocol you get completely dark images. At the same time if you > set the threshold value 0.000658 you get the fine mask. > > I am not sure what causes that but I noticed that behaviour happening > sometimes after the execution of the Bayesian polishing. > > Sincerely, > > Dmitry > > > P.s. it will be great to have unbiased protocol for masking > > Or is there any exist already? > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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