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From: Dmitry A. S. <sem...@gm...> - 2020-05-05 13:54:35
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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:Wingdings; panose-1:5 0 0 0 0 0 0 0 0 0;} @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; margin-bottom:.0001pt; 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"><div class=WordSection1><p class=MsoNormal>Dear Grigory,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Yes (please see the attachment), so</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Relion particles extraction protocol (analyze)<span style='font-family:Wingdings'>à</span> then see the particles gallery (open with imageJ) <span style='font-family:Wingdings'>à</span> then the program crashes with the java error.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you!</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal> </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>Tuesday, May 5, 2020 1:41 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] java error opening the extraction particle file with built-in ImageJ</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi,</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Could you be more specific? What is relion extraction file? Sqlite? Mrcs? Star ? What error? </p></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><o:p> </o:p></p><div><div><p class=MsoNormal>On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear colleagues,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>While opening the relion-extraction file with ImageJ, I’m getting the java error.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Are there any options to open this extracted particle file directly from the folder with ImageJ?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I want to do stk from the extracted particles.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<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...> - 2020-05-05 11:40:59
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Hi, Could you be more specific? What is relion extraction file? Sqlite? Mrcs? Star ? What error? On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > While opening the relion-extraction file with ImageJ, I’m getting the java > error. > > Are there any options to open this extracted particle file directly from > the folder with ImageJ? > > I want to do stk from the extracted particles. > > > > Sincerely, > > Dmitry > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry A. S. <sem...@gm...> - 2020-05-05 11:38:06
|
<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; margin-bottom:.0001pt; 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"><div class=WordSection1><div><p class=MsoNormal>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>While opening the relion-extraction file with ImageJ, I’m getting the java error.</p><p class=MsoNormal>Are there any options to open this extracted particle file directly from the folder with ImageJ?</p><p class=MsoNormal>I want to do stk from the extracted particles.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p></div><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></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></body></html> |
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From: Marta M. <mm...@cn...> - 2020-05-04 07:30:20
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Hi all, try to use the scipion protocol export_to_DB, it saves all the files you need to submit to EMDB in a directory in the right format for submitting. Wbw, MARTA Quoting Grigory Sharov <sha...@gm...>: > Hi Dmitry, > > Scipion does not create output mrc files, Relion does. Afaik, the pixel > size has been written by Relion in the output mrc files since many years. > So, unless you modified the output mrc in some way I don't see how it is > possible for this problem o happen. > > I've just created a test deposition and uploaded Relion in Scipion output > mrc map from 3D refinement without any issues. The website asks you to > provide pixel size and contour level anyway. > > 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, Apr 24, 2020 at 11:00 AM Dmitry A. Semchonok <sem...@gm...> > wrote: > >> Dear colleagues, >> >> >> >> There is an issue while depositing maps to the >> >> https://deposit-pdbe.wwpdb.org/deposition/ >> >> >> >> After you load the maps – the website doesn’t except them. >> >> The error message is that they are it the wrong format. But they are not. >> >> >> >> So >> >> The maps were obtained in the relion 3D auto-refinement. >> >> And it seems that the info about pixel size / box-size is missing. >> Therefore the website - >> >> https://deposit-pdbe.wwpdb.org/deposition/ can not read it. >> >> >> >> I will try >> >> >> >> relion_image_handler --i INPUTMAP.mrc --o OUTPUTMAP.mrc --angpix XXX >> --new_box >> >> >> >> If this is the reason and the cure mentioned above helps I will report >> after. >> >> >> >> Is it possible to fix that issue for the future from the SCIPION directly >> (to get the maps with readable parameters for >> https://deposit-pdbe.wwpdb.org) ? >> >> >> >> Thank you! >> >> >> >> Sincerely, >> >> Dmitry >> >> >> >> >> >> >> >> >> >> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for >> Windows 10 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mm...@cn... |
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From: Grigory S. <sha...@gm...> - 2020-05-02 16:17:38
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Hi Dmitry, Scipion does not create output mrc files, Relion does. Afaik, the pixel size has been written by Relion in the output mrc files since many years. So, unless you modified the output mrc in some way I don't see how it is possible for this problem o happen. I've just created a test deposition and uploaded Relion in Scipion output mrc map from 3D refinement without any issues. The website asks you to provide pixel size and contour level anyway. 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, Apr 24, 2020 at 11:00 AM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > There is an issue while depositing maps to the > > https://deposit-pdbe.wwpdb.org/deposition/ > > > > After you load the maps – the website doesn’t except them. > > The error message is that they are it the wrong format. But they are not. > > > > So > > The maps were obtained in the relion 3D auto-refinement. > > And it seems that the info about pixel size / box-size is missing. > Therefore the website - > > https://deposit-pdbe.wwpdb.org/deposition/ can not read it. > > > > I will try > > > > relion_image_handler --i INPUTMAP.mrc --o OUTPUTMAP.mrc --angpix XXX > --new_box > > > > If this is the reason and the cure mentioned above helps I will report > after. > > > > Is it possible to fix that issue for the future from the SCIPION directly > (to get the maps with readable parameters for > https://deposit-pdbe.wwpdb.org) ? > > > > Thank you! > > > > Sincerely, > > Dmitry > > > > > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry A. S. <sem...@gm...> - 2020-04-24 10:00:31
|
<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; margin-bottom:.0001pt; 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; font-family:"Calibri",sans-serif;} @page WordSection1 {size:8.5in 11.0in; margin:56.7pt 42.5pt 56.7pt 85.05pt;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>There is an issue while depositing maps to the </p><p class=MsoNormal><a href="https://deposit-pdbe.wwpdb.org/deposition/">https://deposit-pdbe.wwpdb.org/deposition/</a></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>After you load the maps – the website doesn’t except them.</p><p class=MsoNormal>The error message is that they are it the wrong format. But they are not.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>So</p><p class=MsoNormal>The maps were obtained in the relion 3D auto-refinement.</p><p class=MsoNormal> And it seems that the info about pixel size / box-size is missing. Therefore the website - </p><p class=MsoNormal><a href="https://deposit-pdbe.wwpdb.org/deposition/">https://deposit-pdbe.wwpdb.org/deposition/</a> can not read it.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I will try </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> relion_image_handler --i INPUTMAP.mrc --o OUTPUTMAP.mrc --angpix XXX --new_box</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>If this is the reason and the cure mentioned above helps I will report after.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is it possible to fix that issue for the future from the SCIPION directly (to get the maps with readable parameters for https://deposit-pdbe.wwpdb.org) ?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you!</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</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><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></body></html> |
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From: Carlos O. S. <co...@cn...> - 2020-04-07 13:44:54
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Dear Dmitry, after computing the class averages there is no way to correct for the CTF of the particles. It is better to use a program that uses it explicitly, as Relion or CryoSparc, or to correct for it before entering in the classification, as Xmipp Wiener filter. Kind regards, Carlos Oscaar On 4/7/20 1:53 PM, Dmitry A. Semchonok wrote: > > Dear colleagues, > > Is there a way to correct the 2D class averages if the CTF parameters > of the single particles are known? > > Thank you! > > Sincerely, > > Dmitry > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2020-04-07 12:21:33
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Run relion 2d classification? 🙂 On Tue, Apr 7, 2020, 12:54 Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > Is there a way to correct the 2D class averages if the CTF parameters of > the single particles are known? > > > > Thank you! > > > > Sincerely, > > Dmitry > > > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry A. S. <sem...@gm...> - 2020-04-07 11:53:56
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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; margin-bottom:.0001pt; 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:56.7pt 42.5pt 56.7pt 85.05pt;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Dear colleagues, </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is there a way to correct the 2D class averages if the CTF parameters of the single particles are known?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you!</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</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><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></body></html> |
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From: Carlos O. S. <co...@cn...> - 2020-03-26 08:47:18
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Dear Veli, I would say this is something internal of Relion and Scipion cannot do much about it. Adding noise to an input signal is not the best you can do in image processing and you may not have the desired result either. Alternatively, what you can do is to use other 2D classifiers. In Scipion you have the ones of CryoSparc, Xmipp, and Eman. The Xmipp one is based on CPU and takes time, but its results are pretty accurate. Kind regards, Carlos Oscar On 3/25/20 11:19 PM, Veli-Pekka Kestilä wrote: > Hi, > > I have problem when running Relion 2D classification with setting of: > > When running with option: Mask particles with zeros? No, fill with > random noise > > Run ends with out of memory error on GPU: > 00112: KERNEL_ERROR: out of memory in > /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/utilities_impl.h > at line 253 (error-code 2) > 00113: in: > /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/cuda/cuda_settings.h, > line 81 > 00114: in: > /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/cuda/cuda_settings.h, > line 81 > 00115: slave 2 encountered error: === Backtrace === > 00116: > /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) > [0x447ce1] > 00117: > /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0xe8) > [0x5cbb48] > 00118: > /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_Z11_threadMainPv+0x3f) > [0x48fbcf] > 00119: /lib64/libpthread.so.0(+0x7e65) [0x7f6e6b492e65] > 00120: /lib64/libc.so.6(clone+0x6d) [0x7f6e6b1bb88d] > > Run works when selecting: Yes, fill with zeroes (but the result isn't > what is hoped for). > > Is there known fix for this situation? There was similar bug in Relion > bug tracker, but it was closed without explanation. > > Specifications are: > System: CentOS Linux release 7.7.1908 (Core) > GPU: 2 x Tesla P100 > Memory: 128GB > CPU: Intel(R) Xeon(R) Gold 5115 CPU @ 2.40GHz > > Scipion is v2.0 (2019-04-23) > Relion 3.0 is compiled against cuda-8.0 > > Greetings, > Veli-Pekka Kestilä > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Veli-Pekka K. <sc...@gu...> - 2020-03-25 23:19:50
|
Hi, I have problem when running Relion 2D classification with setting of: When running with option: Mask particles with zeros? No, fill with random noise Run ends with out of memory error on GPU: 00112: KERNEL_ERROR: out of memory in /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/utilities_impl.h at line 253 (error-code 2) 00113: in: /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/cuda/cuda_settings.h, line 81 00114: in: /data/opt/sci/scipion-2.0/software/em/relion-3.0/src/acc/cuda/cuda_settings.h, line 81 00115: slave 2 encountered error: === Backtrace === 00116: /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x447ce1] 00117: /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0xe8) [0x5cbb48] 00118: /data/opt/sci/scipion-2.0/software/em/relion-3.0/bin/relion_refine_mpi(_Z11_threadMainPv+0x3f) [0x48fbcf] 00119: /lib64/libpthread.so.0(+0x7e65) [0x7f6e6b492e65] 00120: /lib64/libc.so.6(clone+0x6d) [0x7f6e6b1bb88d] Run works when selecting: Yes, fill with zeroes (but the result isn't what is hoped for). Is there known fix for this situation? There was similar bug in Relion bug tracker, but it was closed without explanation. Specifications are: System: CentOS Linux release 7.7.1908 (Core) GPU: 2 x Tesla P100 Memory: 128GB CPU: Intel(R) Xeon(R) Gold 5115 CPU @ 2.40GHz Scipion is v2.0 (2019-04-23) Relion 3.0 is compiled against cuda-8.0 Greetings, Veli-Pekka Kestilä |
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From: Jorge <jji...@cn...> - 2020-03-17 08:37:30
|
Hi Faisal, The datasets are automatically downloaded when a running test needs them. I think this could be a good starting point. https://scipion-em.github.io/docs/docs/developer/running-tests.html?highlight=running%20tests On the other hand, the command 'scipion tutorial intro' is referred to be written in a terminal (command line). On that command, 'scipion' is an alias, which can be created in the bashrc file or can be directly executed in the terminal as 'PATH_TO_YOUR_SCIPION_INSTALLATION_DIR/scipion tutorial intro'. All datasets downloaded will be stored at PATH_TO_YOUR_SCIPION_INSTALLATION_DIR/scipion/data/tests. Hope it helps. Best regards, Jorge On 17/3/20 7:04, khaja faisal tarique wrote: > Dear community members > > I am a new user of Scipion and trying to learn the workflow of single > particle cryoEM by myself. I have installed Scipion 2.0 on my linux > system and now want to download some test datasets from the tutorial > section. But i don't know how to download these files. lets say if I > want to do a reconstruction of a viral capsid or Apoferritin or Bgal, > then according to the tutorial I only need to type: > > scipion tutorial intro > > This command will download (if this was not done earlier) the test > data in direc- > > tory > > > $SCIPION_HOME/data/tests/xmipp_tutorial > > > My question is where to type this command and what sets of path I > should follow to download it. Can it be done through Scipion GUI > (similar to Phenix or ccpem) or it has to be done through the terminal. > > > Please help me out in downloading these test datasets. Being a new > user and having limited knowledge of Linux commands I am stuck. > > > -- > Best Regards > > Faisal > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: khaja f. t. <kha...@gm...> - 2020-03-17 08:33:00
|
Alright..Tahnk you very much Best Regards Faisal On Tue, 17 Mar 2020, 1:53 pm Pablo Conesa, <pc...@cn...> wrote: > "./scipion tutorial *i**ntro*" should download: xmipp_tutorial dataset > > Looking at the code, that would be the only one that downloads a dataset > > > If you want some datasets you can: > > > 1.- Download any from test datasets typing: > > *./scipion testdata list* > > and then > > *./scipion testdata --download <name of the dataset as listed>* > > > 2.- You can download any dataset from EMPIAR: e.g.: > https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10200/ > > > On 17/3/20 8:04, khaja faisal tarique wrote: > > Hi Pconesa > > I haven't tried it but now going to do. One question. Will it download all > the datasets from different projects (Bgal/ApoF/BPV) or just anyone of > these. > > Thanks > > On Tue, Mar 17, 2020 at 12:16 PM <pc...@cn...> wrote: > >> Have you tried to type : >> >> cd path/to/where/you've/installed/scipion >> >> ./scipion tutorial intro >> >> In a terminal window (black ones) >> ase >> El 17 mar. 2020 7:04, khaja faisal tarique <kha...@gm...> >> escribió: >> >> Dear community members >> >> I am a new user of Scipion and trying to learn the workflow of single >> particle cryoEM by myself. I have installed Scipion 2.0 on my linux system >> and now want to download some test datasets from the tutorial section. But >> i don't know how to download these files. lets say if I want to do a >> reconstruction of a viral capsid or Apoferritin or Bgal, then according to >> the tutorial I only need to type: >> >> scipion tutorial intro >> >> This command will download (if this was not done earlier) the test data >> in direc- >> >> tory >> >> >> $SCIPION_HOME/data/tests/xmipp_tutorial >> >> >> My question is where to type this command and what sets of path I should >> follow to download it. Can it be done through Scipion GUI (similar to >> Phenix or ccpem) or it has to be done through the terminal. >> >> >> Please help me out in downloading these test datasets. Being a new user >> and having limited knowledge of Linux commands I am stuck. >> >> -- >> Best Regards >> >> Faisal >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > -- > Faisal Tarique Khaja > Research Associate > Indian Institute of Science > Bangalore, India > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2020-03-17 08:23:12
|
"./scipion tutorial *i**ntro*" should download: xmipp_tutorial dataset Looking at the code, that would be the only one that downloads a dataset If you want some datasets you can: 1.- Download any from test datasets typing: *./scipion testdata list* and then *./scipion testdata --download <name of the dataset as listed>* 2.- You can download any dataset from EMPIAR: e.g.: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10200/ On 17/3/20 8:04, khaja faisal tarique wrote: > Hi Pconesa > > I haven't tried it but now going to do. One question. Will it download > all the datasets from different projects (Bgal/ApoF/BPV) or just > anyone of these. > > Thanks > > On Tue, Mar 17, 2020 at 12:16 PM <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Have you tried to type : > > cd path/to/where/you've/installed/scipion > > ./scipion tutorial intro > > In a terminal window (black ones) > ase > El 17 mar. 2020 7:04, khaja faisal tarique > <kha...@gm... > <mailto:kha...@gm...>> escribió: > > Dear community members > > I am a new user of Scipion and trying to learn the workflow of > single particle cryoEM by myself. I have installed Scipion 2.0 > on my linux system and now want to download some test datasets > from the tutorial section. But i don't know how to download > these files. lets say if I want to do a reconstruction of a > viral capsid or Apoferritin or Bgal, then according to the > tutorial I only need to type: > > scipion tutorial intro > > This command will download (if this was not done earlier) the > test data in direc- > > tory > > > $SCIPION_HOME/data/tests/xmipp_tutorial > > > My question is where to type this command and what sets of > path I should follow to download it. Can it be done through > Scipion GUI (similar to Phenix or ccpem) or it has to be done > through the terminal. > > > Please help me out in downloading these test datasets. Being a > new user and having limited knowledge of Linux commands I am > stuck. > > > -- > Best Regards > > Faisal > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > -- > Faisal Tarique Khaja > Research Associate > Indian Institute of Science > Bangalore, India > > > _______________________________________________ > 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: khaja f. t. <kha...@gm...> - 2020-03-17 07:04:44
|
Hi Pconesa I haven't tried it but now going to do. One question. Will it download all the datasets from different projects (Bgal/ApoF/BPV) or just anyone of these. Thanks On Tue, Mar 17, 2020 at 12:16 PM <pc...@cn...> wrote: > Have you tried to type : > > cd path/to/where/you've/installed/scipion > > ./scipion tutorial intro > > In a terminal window (black ones) > > El 17 mar. 2020 7:04, khaja faisal tarique <kha...@gm...> > escribió: > > Dear community members > > I am a new user of Scipion and trying to learn the workflow of single > particle cryoEM by myself. I have installed Scipion 2.0 on my linux system > and now want to download some test datasets from the tutorial section. But > i don't know how to download these files. lets say if I want to do a > reconstruction of a viral capsid or Apoferritin or Bgal, then according to > the tutorial I only need to type: > > scipion tutorial intro > > This command will download (if this was not done earlier) the test data in > direc- > > tory > > > $SCIPION_HOME/data/tests/xmipp_tutorial > > > My question is where to type this command and what sets of path I should > follow to download it. Can it be done through Scipion GUI (similar to > Phenix or ccpem) or it has to be done through the terminal. > > > Please help me out in downloading these test datasets. Being a new user > and having limited knowledge of Linux commands I am stuck. > > -- > Best Regards > > Faisal > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > -- Faisal Tarique Khaja Research Associate Indian Institute of Science Bangalore, India |
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From: <pc...@cn...> - 2020-03-17 06:46:01
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<div dir='auto'>Have you tried to type :<div dir="auto"><br></div><div dir="auto">cd path/to/where/you've/installed/scipion<br><div dir="auto"><br></div><div dir="auto">./scipion tutorial intro</div><div dir="auto"><br></div><div dir="auto">In a terminal window (black ones)</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">El 17 mar. 2020 7:04, khaja faisal tarique <kha...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr">Dear community members<div><br /></div><div>I am a new user of Scipion and trying to learn the workflow of single particle cryoEM by myself. I have installed Scipion 2.0 on my linux system and now want to download some test datasets from the tutorial section. But i don't know how to download these files. lets say if I want to do a reconstruction of a viral capsid or Apoferritin or Bgal, then according to the tutorial I only need to type<font face="Helvetica"><span style="font-size:12px">:</span></font></div><div><font face="Helvetica"><span style="font-size:12px"><br /></span></font></div><div><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">scipion tutorial intro</p> <p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">This command will download (if this was not done earlier) the test data in direc-</p> <p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">tory</p> <p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'"><br /></p><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">$SCIPION_HOME/data/tests/xmipp_tutorial</p><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'"><br /></p><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">My question is where to type this command and what sets of path I should follow to download it. Can it be done through Scipion GUI (similar to Phenix or ccpem) or it has to be done through the terminal.</p><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'"><br /></p><p style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:'helvetica'">Please help me out in downloading these test datasets. Being a new user and having limited knowledge of Linux commands I am stuck.</p><div><br /></div>-- <br /><div dir="ltr"><div dir="ltr"><div><div dir="ltr">Best Regards</div></div><div dir="ltr"><br /></div><div>Faisal</div></div></div></div></div></div> </blockquote></div><br></div> |
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From: khaja f. t. <kha...@gm...> - 2020-03-17 06:05:14
|
Dear community members I am a new user of Scipion and trying to learn the workflow of single particle cryoEM by myself. I have installed Scipion 2.0 on my linux system and now want to download some test datasets from the tutorial section. But i don't know how to download these files. lets say if I want to do a reconstruction of a viral capsid or Apoferritin or Bgal, then according to the tutorial I only need to type: scipion tutorial intro This command will download (if this was not done earlier) the test data in direc- tory $SCIPION_HOME/data/tests/xmipp_tutorial My question is where to type this command and what sets of path I should follow to download it. Can it be done through Scipion GUI (similar to Phenix or ccpem) or it has to be done through the terminal. Please help me out in downloading these test datasets. Being a new user and having limited knowledge of Linux commands I am stuck. -- Best Regards Faisal |
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From: Philip R. B. <pr...@gm...> - 2020-03-09 18:41:03
|
Hi David,
I tried moving the libraries as suggested in the Sep 5th 2019 thread.
I moved librariies around as suggested. Now I get below.
Ubuntu version is
> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.1 LTS
Release: 18.04
Codename: bionic
-----------------------------------------------------------
Scipion v2.0 (2019-04-23) Diocletian
>>>>> python /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py
Xmipp installation have failed or xmipp's C++ binnding have some problem:
/home/software/SCIPION/scipion/software/em/xmipp/lib/libXmipp.so: undefined
symbol: _ZNK2H56H5File14throwExceptionERKSsS2_
> Please, remove the Xmipp installation (usually 'rm software/em/xmipp')
and re-install it
Traceback (most recent call last):
File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py", line
32, in <module>
from pyworkflow.gui.project import ProjectManagerWindow
File "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py",
line 27, in <module>
from project import ProjectManagerWindow, ProjectWindow
File "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py",
line 45, in <module>
from pyworkflow.project import MenuConfig, ProjectSettings
File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py",
line 28, in <module>
from .project import Project, MissingProjectDbException
File "/home/software/SCIPION/scipion/pyworkflow/project/project.py", line
37, in <module>
import pyworkflow.em as em
File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line 31,
in <module>
from data import *
File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36, in
<module>
from convert import ImageHandler
File "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py",
line 28, in <module>
from .image_handler import ImageHandler, DT_FLOAT
File
"/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py",
line 38, in <module>
sys.exit(-1)
NameError: name 'sys' is not defined
On Mon, Mar 9, 2020 at 6:46 AM David Maluenda <dma...@cn...> wrote:
> Hi again Philip,
>
> I've just realized that a similar error was reported in this github-issue
> <https://github.com/I2PC/scipion-em-xmipp/issues/148>. Take it into
> account.
>
> Thanks to report and don't hesitate to contact us if still not working.
>
> <http://ucm.es/>
>
> *_____Dr. David Maluenda Niubó*
> dma...@cn... - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
> BioComputing Unit <http://biocomputingunit.es/>
>
> 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 Mon, Mar 9, 2020 at 11:39 AM David Maluenda <dma...@cn...>
> wrote:
>
>> Hi Philip, thanks for reporting
>>
>> This error usually raise when installing xmippBin_Centos in a debian
>> distro or the opposite.
>>
>> Which OS is the system?
>>
>> If you get the same or similar error when installing the other
>> xmippBin_xxx, then I will recommend you to install Scipion and Xmipp from
>> sources.
>>
>>
>> Kind regards,
>>
>> <http://ucm.es/>
>>
>> *_____Dr. David Maluenda Niubó*Hi
>> dma...@cn... - (+34) 619 029 310
>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>> BioComputing Unit <http://biocomputingunit.es/>
>>
>> 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 Mon, Mar 9, 2020 at 5:26 AM Philip R. Baldwin <pr...@gm...>
>> wrote:
>>
>>> Hi Everyone,
>>> I am sure it is an old topic, but I am having trouble installing xmipp
>>> underneath
>>> scipion which seemed to install quite nicely at the high level.
>>>
>>> Here is the scipion error after xmipp installation through the scipion
>>> gui.
>>>
>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>> Scipion v2.0 (2019-04-23) Diocletian
>>>
>>> >>>>> python
>>> /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py
>>>
>>> Xmipp installation have failed or xmipp's C++ binnding have some problem:
>>> /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3: undefined symbol:
>>> fftw_set_planner_hooks
>>>
>>> > Please, remove the Xmipp installation (usually 'rm
>>> software/em/xmipp') and re-install it
>>>
>>> Traceback (most recent call last):
>>> File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py",
>>> line 32, in <module>
>>> from pyworkflow.gui.project import ProjectManagerWindow
>>> File
>>> "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py", line
>>> 27, in <module>
>>> from project import ProjectManagerWindow, ProjectWindow
>>> File
>>> "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py", line
>>> 45, in <module>
>>> from pyworkflow.project import MenuConfig, ProjectSettings
>>> File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py",
>>> line 28, in <module>
>>> from .project import Project, MissingProjectDbException
>>> File "/home/software/SCIPION/scipion/pyworkflow/project/project.py",
>>> line 37, in <module>
>>> import pyworkflow.em as em
>>> File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line
>>> 31, in <module>
>>> from data import *
>>> File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36,
>>> in <module>
>>> from convert import ImageHandler
>>> File
>>> "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py", line
>>> 28, in <module>
>>> from .image_handler import ImageHandler, DT_FLOAT
>>> File
>>> "/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py",
>>> line 38, in <module>
>>> sys.exit(-1)
>>> NameError: name 'sys' is not defined
>>>
>>>
>>> --------------------------------------------------------------------------------------------
>>>
>>> Thank you in advance,
>>>
>>> Philip Baldwin
>>> The Salk Institute
>>> _______________________________________________
>>> 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
>
|
|
From: David M. <dma...@cn...> - 2020-03-09 13:46:09
|
Hi again Philip, I've just realized that a similar error was reported in this github-issue <https://github.com/I2PC/scipion-em-xmipp/issues/148>. Take it into account. Thanks to report and don't hesitate to contact us if still not working. <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> 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 Mon, Mar 9, 2020 at 11:39 AM David Maluenda <dma...@cn...> wrote: > Hi Philip, thanks for reporting > > This error usually raise when installing xmippBin_Centos in a debian > distro or the opposite. > > Which OS is the system? > > If you get the same or similar error when installing the other > xmippBin_xxx, then I will recommend you to install Scipion and Xmipp from > sources. > > > Kind regards, > > <http://ucm.es/> > > *_____Dr. David Maluenda Niubó*Hi > dma...@cn... - (+34) 619 029 310 > CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> > BioComputing Unit <http://biocomputingunit.es/> > > 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 Mon, Mar 9, 2020 at 5:26 AM Philip R. Baldwin <pr...@gm...> > wrote: > >> Hi Everyone, >> I am sure it is an old topic, but I am having trouble installing xmipp >> underneath >> scipion which seemed to install quite nicely at the high level. >> >> Here is the scipion error after xmipp installation through the scipion >> gui. >> >> >> --------------------------------------------------------------------------------------------------------------------------------------------------- >> >> Scipion v2.0 (2019-04-23) Diocletian >> >> >>>>> python /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py >> >> Xmipp installation have failed or xmipp's C++ binnding have some problem: >> /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3: undefined symbol: >> fftw_set_planner_hooks >> >> > Please, remove the Xmipp installation (usually 'rm >> software/em/xmipp') and re-install it >> >> Traceback (most recent call last): >> File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py", >> line 32, in <module> >> from pyworkflow.gui.project import ProjectManagerWindow >> File >> "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py", line >> 27, in <module> >> from project import ProjectManagerWindow, ProjectWindow >> File >> "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py", line >> 45, in <module> >> from pyworkflow.project import MenuConfig, ProjectSettings >> File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py", >> line 28, in <module> >> from .project import Project, MissingProjectDbException >> File "/home/software/SCIPION/scipion/pyworkflow/project/project.py", >> line 37, in <module> >> import pyworkflow.em as em >> File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line >> 31, in <module> >> from data import * >> File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36, >> in <module> >> from convert import ImageHandler >> File >> "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py", line >> 28, in <module> >> from .image_handler import ImageHandler, DT_FLOAT >> File >> "/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py", >> line 38, in <module> >> sys.exit(-1) >> NameError: name 'sys' is not defined >> >> >> -------------------------------------------------------------------------------------------- >> >> Thank you in advance, >> >> Philip Baldwin >> The Salk Institute >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > |
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From: David M. <dma...@cn...> - 2020-03-09 10:40:45
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Hi Philip, thanks for reporting This error usually raise when installing xmippBin_Centos in a debian distro or the opposite. Which OS is the system? If you get the same or similar error when installing the other xmippBin_xxx, then I will recommend you to install Scipion and Xmipp from sources. Kind regards, <http://ucm.es/> *_____Dr. David Maluenda Niubó*Hi dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> 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 Mon, Mar 9, 2020 at 5:26 AM Philip R. Baldwin <pr...@gm...> wrote: > Hi Everyone, > I am sure it is an old topic, but I am having trouble installing xmipp > underneath > scipion which seemed to install quite nicely at the high level. > > Here is the scipion error after xmipp installation through the scipion > gui. > > > --------------------------------------------------------------------------------------------------------------------------------------------------- > > Scipion v2.0 (2019-04-23) Diocletian > > >>>>> python /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py > > Xmipp installation have failed or xmipp's C++ binnding have some problem: > /usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3: undefined symbol: > fftw_set_planner_hooks > > > Please, remove the Xmipp installation (usually 'rm software/em/xmipp') > and re-install it > > Traceback (most recent call last): > File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py", > line 32, in <module> > from pyworkflow.gui.project import ProjectManagerWindow > File > "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py", line > 27, in <module> > from project import ProjectManagerWindow, ProjectWindow > File "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py", > line 45, in <module> > from pyworkflow.project import MenuConfig, ProjectSettings > File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py", > line 28, in <module> > from .project import Project, MissingProjectDbException > File "/home/software/SCIPION/scipion/pyworkflow/project/project.py", > line 37, in <module> > import pyworkflow.em as em > File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line > 31, in <module> > from data import * > File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36, in > <module> > from convert import ImageHandler > File "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py", > line 28, in <module> > from .image_handler import ImageHandler, DT_FLOAT > File > "/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py", > line 38, in <module> > sys.exit(-1) > NameError: name 'sys' is not defined > > > -------------------------------------------------------------------------------------------- > > Thank you in advance, > > Philip Baldwin > The Salk Institute > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Philip R. B. <pr...@gm...> - 2020-03-09 04:26:27
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Hi Everyone,
I am sure it is an old topic, but I am having trouble installing xmipp
underneath
scipion which seemed to install quite nicely at the high level.
Here is the scipion error after xmipp installation through the scipion gui.
---------------------------------------------------------------------------------------------------------------------------------------------------
Scipion v2.0 (2019-04-23) Diocletian
>>>>> python /home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py
Xmipp installation have failed or xmipp's C++ binnding have some problem:
/usr/lib/x86_64-linux-gnu/libfftw3_threads.so.3: undefined symbol:
fftw_set_planner_hooks
> Please, remove the Xmipp installation (usually 'rm software/em/xmipp')
and re-install it
Traceback (most recent call last):
File "/home/software/SCIPION/scipion/pyworkflow/apps/pw_manager.py", line
32, in <module>
from pyworkflow.gui.project import ProjectManagerWindow
File "/home/software/SCIPION/scipion/pyworkflow/gui/project/__init__.py",
line 27, in <module>
from project import ProjectManagerWindow, ProjectWindow
File "/home/software/SCIPION/scipion/pyworkflow/gui/project/project.py",
line 45, in <module>
from pyworkflow.project import MenuConfig, ProjectSettings
File "/home/software/SCIPION/scipion/pyworkflow/project/__init__.py",
line 28, in <module>
from .project import Project, MissingProjectDbException
File "/home/software/SCIPION/scipion/pyworkflow/project/project.py", line
37, in <module>
import pyworkflow.em as em
File "/home/software/SCIPION/scipion/pyworkflow/em/__init__.py", line 31,
in <module>
from data import *
File "/home/software/SCIPION/scipion/pyworkflow/em/data.py", line 36, in
<module>
from convert import ImageHandler
File "/home/software/SCIPION/scipion/pyworkflow/em/convert/__init__.py",
line 28, in <module>
from .image_handler import ImageHandler, DT_FLOAT
File
"/home/software/SCIPION/scipion/pyworkflow/em/convert/image_handler.py",
line 38, in <module>
sys.exit(-1)
NameError: name 'sys' is not defined
--------------------------------------------------------------------------------------------
Thank you in advance,
Philip Baldwin
The Salk Institute
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From: Dmitry A. S. <sem...@gm...> - 2020-03-07 09:42:58
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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:Wingdings; panose-1:5 0 0 0 0 0 0 0 0 0;} @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; margin-bottom:.0001pt; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph {mso-style-priority:34; margin-top:0in; margin-right:0in; margin-bottom:8.0pt; margin-left:.5in; mso-add-space:auto; line-height:106%; font-size:11.0pt; font-family:"Calibri",sans-serif;} p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst {mso-style-priority:34; mso-style-type:export-only; margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; mso-add-space:auto; line-height:106%; font-size:11.0pt; font-family:"Calibri",sans-serif;} p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle {mso-style-priority:34; mso-style-type:export-only; margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; mso-add-space:auto; line-height:106%; font-size:11.0pt; font-family:"Calibri",sans-serif;} p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast {mso-style-priority:34; mso-style-type:export-only; margin-top:0in; margin-right:0in; margin-bottom:8.0pt; margin-left:.5in; mso-add-space:auto; line-height:106%; font-size:11.0pt; font-family:"Calibri",sans-serif;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:56.7pt 42.5pt 56.7pt 85.05pt;} div.WordSection1 {page:WordSection1;} /* List Definitions */ @list l0 {mso-list-id:435516352; mso-list-type:hybrid; mso-list-template-ids:-47823158 769978228 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;} @list l0:level1 {mso-level-start-at:0; mso-level-number-format:bullet; mso-level-text:-; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:"Calibri",sans-serif; mso-fareast-font-family:Calibri;} @list l0:level2 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:"Courier New";} @list l0:level3 {mso-level-number-format:bullet; mso-level-text:\F0A7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:Wingdings;} @list l0:level4 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:Symbol;} @list l0:level5 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:"Courier New";} @list l0:level6 {mso-level-number-format:bullet; mso-level-text:\F0A7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:Wingdings;} @list l0:level7 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:Symbol;} @list l0:level8 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:"Courier New";} @list l0:level9 {mso-level-number-format:bullet; mso-level-text:\F0A7; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in; font-family:Wingdings;} ol {margin-bottom:0in;} ul {margin-bottom:0in;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The question is about <b>xmipp-create gallery </b>protocol. </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have a spherical map. I want to project is as such that there will be no repeatable projections and all the map was covered. </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The <b>xmipp-create gallery</b> protocol has a rotational angle & tilt angle options.</p><p class=MsoNormal>When I try to set any of those parameters to 0 (Min: 0; max: 0), I get an error.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Is that right that to get unrepeatable projections of my spherical map I need to select: </p><ul style='margin-top:0in' type=disc><li class=MsoListParagraphCxSpFirst style='margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1'>for Rotational angle Min 0 Max 360 (step for example 30) </li><li class=MsoListParagraphCxSpLast style='margin-left:0in;mso-add-space:auto;mso-list:l0 level1 lfo1'>for Tilt angle Min 0 Max 90; (step 30)?</li></ul><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you!</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</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></body></html> |
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From: Jose M. de la R. T. <del...@gm...> - 2020-03-02 09:35:27
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Hi Dmitry, There is a protocol 'assing - ctf' that does exactly what you want. You can use previously estimated CTFs and then assign it to another set (or subset) of micrographs and particles, assuming it comes from the same processing branch. Best regards, Jose Miguel On Mon, Mar 2, 2020 at 10:32 AM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > I want to apply the estimated ctf parameters to the micrographs and > extracted particles. > > How is it possible? > > 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...> - 2020-03-02 09:32:26
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Dear colleagues, I want to apply the estimated ctf parameters to the micrographs and extracted particles. How is it possible? Thank you! Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2020-03-01 07:53:10
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Dear Dmitry, there are several tools. You can make a subtraction of the two volumes (Tools - Operate), or you can compare them in Fourier (look for, Ctrl-F, resolution; you will find xmipp 3D resolution). This will allow you to compute the FSC between the two. Before comparing them, make sure that they are well aligned (ctrl-F, align volumes). At the moment, these are the tools that come to my mind. Kind regards, Carlos Oscar El 28/02/2020 a las 10:56, Dmitry Semchonok escribió: > Dear colleagues, > > I have similar cryo-em maps that have also some differences. > I want to compare them > > Is there a tool in SCIPION that can compare the cryo-em maps? > > Thank you! > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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