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From: Dmitry S. <Sem...@gm...> - 2021-03-17 13:42:29
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Dear Yunior, dear colleagues, I hope you could help me. Error in SCIPION3 during crysparc2 – global ctf refinement. When I change the “Number of iterations” parameter in the crysparc2 – global ctf refinement to 2…or.4…or….8….(more than 1) SCIPION3 gives the error: 00037: STARTED: createOutputStep, step 3, time 2021-03-17 14:22:18.663183 00038: Detected CryoSPARC 2+ .cs file 00039: Traceback (most recent call last): 00040: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 189, in run 00041: self._run() 00042: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run 00043: resultFiles = self._runFunc() 00044: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc 00045: return self._func(*self._args) 00046: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 227, in createOutputStep 00047: convertCs2Star(args) 00048: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 51, in convertCs2Star 00049: cs = np.load(args.input[0]) 00050: File "/home/user/miniconda3/envs/scipion3/lib/python3.8/site-packages/numpy/lib/npyio.py", line 428, in load 00051: fid = open(os_fspath(file), "rb") 00052: FileNotFoundError: [Errno 2] No such file or directory: 'Runs/006620_ProtCryoSparcGlobalCtfRefinement/extra/J87/particles.cs' 00053: Protocol failed: [Errno 2] No such file or directory: 'Runs/006620_ProtCryoSparcGlobalCtfRefinement/extra/J87/particles.cs' 00054: FAILED: createOutputStep, step 3, time 2021-03-17 14:22:21.455791 00055: *** Last status is failed BUT inside the cryosparc the process finishes without error. Please see the image. When I use 1 (default) value in crysparc2 – global ctf refinement SCIPION3 finishes with no error. What can be the solution for that? Sincerely, Dmitry |
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From: Marta M. <mm...@cn...> - 2021-03-15 16:25:56
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Hi Dmitry, here you are our basic tutorial for modeling in Scipion3: https://raw.githubusercontent.com/scipion-em/docs/release-3.0.0/docs/pdfs/tutorial_model_building_basic.pdf Wbw, MARTA Dmitry Semchonok <Sem...@gm...> escribió: > <>Dear colleagues, > > > > I have an em map and a correspondent model (very similar). > > > > What are the mains steps to fit/refine this model into the map? > > > > > > I look for the simple algorithm (steps//manual) of the model in map > refinement (phenix, ccp4-coot etc.). > > > > Sorry, I am still not knowing very well the model building tab in SCIPION. > > > > > > Sincerely, > > Dmitry -- 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: Dmitry S. <Sem...@gm...> - 2021-03-15 16:10:29
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<>Dear colleagues, I have an em map and a correspondent model (very similar). What are the mains steps to fit/refine this model into the map? I look for the simple algorithm (steps//manual) of the model in map refinement (phenix, ccp4-coot etc.). Sorry, I am still not knowing very well the model building tab in SCIPION. Sincerely, Dmitry |
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From: Pablo C. <pc...@cn...> - 2021-03-12 10:50:21
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Thanks Dmitry. Good to know. On 12/3/21 11:32, Dmitry Semchonok wrote: > Dear colleagues, > > Small Friday observation. > > I just found the reason why the output frames from either "relion-motion correction" or “motioncorr - movie alignment" protocols can be totally black. > > The reason was the the doze "per Frame" in the previous step - "import movies” that was not set correctly (by the user): so, instead of about 1 e/A^2 (depending on the recording settings) or, in my case 0.9856 due to type was set 9856.0 > > Interestingly, even with those wrong settings only xmipp - Flex align (on the same movies dataset) gave the nice output images (not the black ones). :) > > > > > 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...> - 2021-03-12 10:32:49
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Dear colleagues, Small Friday observation. I just found the reason why the output frames from either "relion-motion correction" or “motioncorr - movie alignment" protocols can be totally black. The reason was the the doze "per Frame" in the previous step - "import movies” that was not set correctly (by the user): so, instead of about 1 e/A^2 (depending on the recording settings) or, in my case 0.9856 due to type was set 9856.0 Interestingly, even with those wrong settings only xmipp - Flex align (on the same movies dataset) gave the nice output images (not the black ones). :) Sincerely, Dmitry |
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From: Yunior C. F. R. <cfo...@cn...> - 2021-03-09 16:17:55
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Hi Dmitry, I followed the steps in your email and everything worked for me. I attach an image. For the symmetry expansion algorithm, tomorrow you will have a protocol inside the plugin, hehehehehe. On the other hand, what version of relion do you have installed? I've been reported problems with particles coming from relion3.1, but some CS algorithms require these particles to have CTF and alignment. Do you want us to organise a meeting to see what mistakes you have? Best Regards, Yunior El 8/3/21 a las 21:39, Dmitry A. Semchonok escribió: > > Dear Yunior and all, > > I try to run the local refinement by cryosparc plugin in SCIPION. > > Before that I need to run the symmetry expansion. > > But the cryosparc symmetry expansion plugin is currently not available > in SCIPION. > > So what I tried: > > 1. Run the symmetry expansion in relion. Then the local refinement in > cryosparc. > > But I got the error about the absence of CTF information. > > 2. Run the symmetry expansion in cryosparc as a continuation of for > example 3D -refinement (with debug function on). > > The symmetry expansion works fine. But then the locar refinement in > cryosparc gives an error: > > /Traceback (most recent call last):/ > > / File "cryosparc_worker/cryosparc_compute/run.py", line 84, in > cryosparc_compute.run.main/ > > / File > "cryosparc_worker/cryosparc_compute/jobs/local_refine/newrun.py", line > 116, in cryosparc_compute.jobs.local_refine.newrun.run_local_refine/ > > / File > "/home/panos/software/cryosparc/cryosparc2_worker/cryosparc_compute/particles.py", > line 77, in read_blobs/ > > / with open(abs_path, 'rb') as mrc_file:/ > > /FileNotFoundError: [Errno 2] No such file or directory: > '/home/panos/software/cryosparc/scipion_projects/Fraction_33_Lisa-panos/P18/J129/imported/mic_000001.mrcs'/ > > Is there any possibility to run the local refinement after the > symmetry expansion? > > Thank you. > > Sincerely, > > Dmitry > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > |
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From: Dmitry A. S. <sem...@gm...> - 2021-03-08 20:40:02
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph {mso-style-priority:34; margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; font-size:11.0pt; font-family:"Calibri",sans-serif;} .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;} /* List Definitions */ @list l0 {mso-list-id:531960073; mso-list-type:hybrid; mso-list-template-ids:-2011270814 -1 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} @list l0:level1 {mso-level-number-format:alpha-lower; mso-level-text:"%1\)"; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level2 {mso-level-number-format:alpha-lower; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level3 {mso-level-number-format:roman-lower; mso-level-tab-stop:none; mso-level-number-position:right; text-indent:-9.0pt;} @list l0:level4 {mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level5 {mso-level-number-format:alpha-lower; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level6 {mso-level-number-format:roman-lower; mso-level-tab-stop:none; mso-level-number-position:right; text-indent:-9.0pt;} @list l0:level7 {mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level8 {mso-level-number-format:alpha-lower; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-.25in;} @list l0:level9 {mso-level-number-format:roman-lower; mso-level-tab-stop:none; mso-level-number-position:right; text-indent:-9.0pt;} ol {margin-bottom:0in;} ul {margin-bottom:0in;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Dear Yunior and all,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>I try to run the local refinement by cryosparc plugin in SCIPION.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>Before that I need to run the symmetry expansion.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>But the cryosparc symmetry expansion plugin is currently not available in SCIPION.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-GB>So what I tried:<o:p></o:p></span></p><ol style='margin-top:0in' start=1 type=a><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'><span lang=EN-GB>Run the symmetry expansion in relion. Then the local refinement in cryosparc.</span></li></ol><p class=MsoNormal>But I got the error about the absence of CTF information.</p><p class=MsoNormal><o:p> </o:p></p><ol style='margin-top:0in' start=2 type=a><li class=MsoListParagraph style='margin-left:0in;mso-list:l0 level1 lfo1'>Run the symmetry expansion in cryosparc as a continuation of for example 3D -refinement (with debug function on).</li></ol><p class=MsoNormal style='margin-left:.25in'>The symmetry expansion works fine. But then the locar refinement in cryosparc gives an error:</p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'><i>Traceback (most recent call last):<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><i> File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><i> File "cryosparc_worker/cryosparc_compute/jobs/local_refine/newrun.py", line 116, in cryosparc_compute.jobs.local_refine.newrun.run_local_refine<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><i> File "/home/panos/software/cryosparc/cryosparc2_worker/cryosparc_compute/particles.py", line 77, in read_blobs<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><i> with open(abs_path, 'rb') as mrc_file:<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><i>FileNotFoundError: [Errno 2] No such file or directory: '/home/panos/software/cryosparc/scipion_projects/Fraction_33_Lisa-panos/P18/J129/imported/mic_000001.mrcs'<o:p></o:p></i></p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'>Is there any possibility to run the local refinement after the symmetry expansion?</p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'>Thank you.</p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.25in'>Sincerely,</p><p class=MsoNormal style='margin-left:.25in'>Dmitry</p><p class=MsoNormal style='margin-left:.25in'><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: Yunior C. F. R. <cfo...@cn...> - 2021-03-08 17:37:11
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Hi Dmitry, I have been checking the execution of this protocol and it is a bit strange that this file is not found, because it is cryoSPARC's own output. I don't get that error. Have you re-launched this protocol? Try a restart. If the error persists, we can look at it when you can. Best Regards Yunior El 8/3/21 a las 14:22, Dmitry Semchonok escribió: > Dear colleagues, > > The cryosparc global CTF fails in SCIPION 3 (but finished correctly in cryosparc itself) with the following error — CryoSPARC 2+ .cs file > > FINISHED: processStep, step 2, time 2021-03-08 14:12:20.142810 > 00037: STARTED: createOutputStep, step 3, time 2021-03-08 14:12:20.173650 > 00038: Detected CryoSPARC 2+ .cs file > 00039: Traceback (most recent call last): > 00040: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run > 00041: self._run() > 00042: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run > 00043: resultFiles = self._runFunc() > 00044: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc > 00045: return self._func(*self._args) > 00046: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 227, in createOutputStep > 00047: convertCs2Star(args) > 00048: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/convert/convert.py", line 51, in convertCs2Star > 00049: cs = np.load(args.input[0]) > 00050: File "/opt/Scipion3/.scipion3env/lib64/python3.6/site-packages/numpy/lib/npyio.py", line 428, in load > 00051: fid = open(os_fspath(file), "rb") > 00052: FileNotFoundError: [Errno 2] No such file or directory: 'Runs/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs' > 00053: Protocol failed: [Errno 2] No such file or directory: 'Runs/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs' > 00054: FAILED: createOutputStep, step 3, time 2021-03-08 14:12:22.171112 > 00055: *** Last status is failed > 00056: ------------------- PROTOCOL FAILED (DONE 3/3) > > > Any advice? > > > Thank you in advance! > > Sincerely, > Dmitry > |
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From: Dmitry S. <Sem...@gm...> - 2021-03-08 13:22:39
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Dear colleagues, The cryosparc global CTF fails in SCIPION 3 (but finished correctly in cryosparc itself) with the following error — CryoSPARC 2+ .cs file FINISHED: processStep, step 2, time 2021-03-08 14:12:20.142810 00037: STARTED: createOutputStep, step 3, time 2021-03-08 14:12:20.173650 00038: Detected CryoSPARC 2+ .cs file 00039: Traceback (most recent call last): 00040: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 189, in run 00041: self._run() 00042: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 240, in _run 00043: resultFiles = self._runFunc() 00044: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/pyworkflow/protocol/protocol.py", line 236, in _runFunc 00045: return self._func(*self._args) 00046: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/protocols/protocol_cryosparc_global_ctf_refinement.py", line 227, in createOutputStep 00047: convertCs2Star(args) 00048: File "/opt/Scipion3/.scipion3env/lib/python3.6/site-packages/cryosparc2/convert/convert.py", line 51, in convertCs2Star 00049: cs = np.load(args.input[0]) 00050: File "/opt/Scipion3/.scipion3env/lib64/python3.6/site-packages/numpy/lib/npyio.py", line 428, in load 00051: fid = open(os_fspath(file), "rb") 00052: FileNotFoundError: [Errno 2] No such file or directory: 'Runs/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs' 00053: Protocol failed: [Errno 2] No such file or directory: 'Runs/005994_ProtCryoSparcGlobalCtfRefinement/extra/J102/particles.cs' 00054: FAILED: createOutputStep, step 3, time 2021-03-08 14:12:22.171112 00055: *** Last status is failed 00056: ------------------- PROTOCOL FAILED (DONE 3/3) Any advice? Thank you in advance! Sincerely, Dmitry |
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From: Jose M. de la R. T. <del...@gm...> - 2021-03-06 08:15:44
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Hi Dmitry, What you should import is a cryolo trained model, not a volume. Then you can use that model instead of the general one. As far as I know, a volume can't be used for picking with cryolo. Best regards, Jose Miguel On Sat, Mar 6, 2021, 8:50 AM Dmitry A. Semchonok <sem...@gm...> wrote: > Dear colleagues, > > > > How does the import sphire – cryolo import works? > > Using this protocol, I imported the volume that I want to use for picking > with shire picking. > > But the shire picking gives an error. > > > > Protocol failed: Command 'eval > "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"&& > conda activate cryolo-1.7.6 && cryolo_predict.py -c > Runs/003144_SphireProtCRYOLOPicking/extra/config.json -w > /data1/ScipionUserData/projects/Fraction_33_Lisa/Runs/003113_SphireProtCryoloImport/extra/cryosparc_P18_J64_005_volume_map.mrc > -i Runs/003144_SphireProtCRYOLOPicking/tmp/micrographs_1-17/ -o > Runs/003144_SphireProtCRYOLOPicking/tmp/micrographs_1-17/ -t 0.200 -g 0 -nc > 4' returned non-zero exit status 1. > > > > > > Could you give any suggestions? > > > > > > 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...> - 2021-03-06 07:50:32
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><div><p class=MsoNormal>Dear colleagues,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>How does the import sphire – cryolo import works?</p><p class=MsoNormal>Using this protocol, I imported the volume that I want to use for picking with shire picking.</p><p class=MsoNormal>But the shire picking gives an error.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='color:red'>Protocol failed: Command 'eval "$(/opt/Scipion3/software/em/eman-2.31/condabin/conda shell.bash hook)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/003144_SphireProtCRYOLOPicking/extra/config.json -w /data1/ScipionUserData/projects/Fraction_33_Lisa/Runs/003113_SphireProtCryoloImport/extra/cryosparc_P18_J64_005_volume_map.mrc -i Runs/003144_SphireProtCRYOLOPicking/tmp/micrographs_1-17/ -o Runs/003144_SphireProtCRYOLOPicking/tmp/micrographs_1-17/ -t 0.200 -g 0 -nc 4' returned non-zero exit status 1.<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Could you give any suggestions?</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></div><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: Dmitry A. S. <sem...@gm...> - 2021-03-04 21:48:39
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><div><p class=MsoNormal><span lang=EN-GB>Dear </span>Yunior<span lang=EN-GB> & all,<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am currently trying to run the cryosparc2 plugin 3D non-uniform refinement.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Since I use the latest available cryosparc with a patch ( 3.1.0+210216), I am getting an error. This error asks me to contact you since the compatibility is not yet tested.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>At the same time, the 3D non-uniform refinement (Legacy) works fine.</p><p class=MsoNormal>Most of the other cryosparc plugins as well.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Could you please have a look at the issue?</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you in advance.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sincerely,</p><p class=MsoNormal>Dmitry</p></div><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...> - 2021-02-24 19:37:12
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Dear Dieter, if you send me the pdb I can try myself and I will try to check where the problem is. Kind regards, Carlos Oscar El 24/02/2021 a las 20:23, Dieter Blaas escribió: > > Thank you all, good to know :-) > > just to add: What might be the reason for the error (see below for > my original post)? > > best, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail:die...@me... > ------------------------------------------------------------------------ > On 24.02.2021 19:41, Carlos Oscar Sorzano wrote: >> >> Dear all, >> >> I totally agree. The most convenient way to create these volumes is >> through the protocol. >> >> Cheers, Carlos Oscar >> >> On 2/24/21 4:31 PM, Pablo Conesa wrote: >>> >>> Hi Dieter, people from xmipp team is reading this list. So is the >>> right email to be used. Although maybe a xmipp specific email could >>> be more clearer. >>> >>> My line was, more than a clarification for you, a call for xmipp >>> team to come to the rescue!. Which Carlos Oscar did. >>> >>> The way you used xmipp through scipion is fine. You could even do it >>> in one line: >>> >>> *scipion3 **xmipp_volume_from_pdb* >>> >>> scipion3 will redirect command starting with "xmipp_*" to xmipp , >>> "e2" or "sx" to eman, and "relion" to relion. >>> >>> I do not know a better way from the command line, unless you want to >>> avoid scipion and use directly xmipp. There is a way, but then you >>> need to install xmipp on its own, which might be more complex. >>> >>> The other way would be using scipion itself, you have a protocol for >>> that, that its calling xmipp program in the backgound: >>> >>> >>> On 24/2/21 13:30, Dieter Blaas wrote: >>>> >>>> Hi Pablo, >>>> >>>> thanks! I thought that this list was the successor of the xmipp >>>> list. Sorry! >>>> >>>> Actually, I created the scipion3 environment with " conda activate >>>> scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am >>>> not sure whether this makes sense as I have been using the old >>>> fashioned command line xmipp commands until I recently had to move >>>> to scipion. >>>> >>>> I was wondering whether there was a better way of getting from pdb >>>> files to volume files to be used as a starting map for relion >>>> refinements or making masks etc. In fact, I appended a number of >>>> pdb files and removed everything not being a coordinate. This file >>>> I then tried to use for making a volume including all atoms.... >>>> >>>> best, Dieter >>>> >>>> ------------------------------------------------------------------------ >>>> Dieter Blaas, >>>> Max Perutz Laboratories >>>> Medical University of Vienna, >>>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>>> Dr. Bohr Gasse 9/3, >>>> A-1030 Vienna, Austria, >>>> Tel: 0043 1 4277 61630, >>>> Mobile: 0043 699 1942 1659 >>>> e-mail:die...@me... >>>> ------------------------------------------------------------------------ >>>> On 23.02.2021 12:37, Pablo Conesa wrote: >>>>> >>>>> Hi Dieter! >>>>> >>>>> I think xmipp team should know more about the current status. >>>>> >>>>> One question, how are you invoking the xmipp command, though >>>>> scipion3?, like scipion3 run xmipp_volume_from_pdb >>>>> >>>>> On 18/2/21 19:20, Dieter Blaas wrote: >>>>>> Hi, >>>>>> >>>>>> I am trying to make a kind of mean volume from many aligned pdb >>>>>> files. I appended all the pdbs and removed everything that is not >>>>>> a coordinate record. This file I feed into xmipp like so: >>>>>> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" >>>>>> "--blobs" "--fixed_Gaussian". I am using an old version of this >>>>>> script but I believe that it has not have changed over the years. >>>>>> I get this: >>>>>> >>>>>> ############################################ >>>>>> >>>>>> PDB file: all_atoms.pdb >>>>>> >>>>>> Sampling rate: 1 >>>>>> High sampling rate: 0.0833333 >>>>>> Size: -1 >>>>>> Center PDB: 0 >>>>>> Do not Hetatm: 0 >>>>>> Use blobs: 1 >>>>>> Use poor Gaussian: 0 >>>>>> Use fixed Gaussian: 1 >>>>>> Intensity Col: occupancy >>>>>> Sigma: -1 >>>>>> >>>>>> Bus error (core dumped) >>>>>> Traceback (most recent call last): >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", line >>>>>> 8, in <module> >>>>>> sys.exit(main()) >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >>>>>> line 43, in main >>>>>> runProgram(program, params) >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >>>>>> line 64, in runProgram >>>>>> pwutils.runJob(None, program, params, env=env) >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>>>> line 51, in runJob >>>>>> return runCommand(command, env, cwd) >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>>>> line 66, in runCommand >>>>>> check_call(command, shell=True, stdout=sys.stdout, >>>>>> stderr=sys.stderr, >>>>>> File >>>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >>>>>> line 364, in check_call >>>>>> raise CalledProcessError(retcode, cmd) >>>>>> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb >>>>>> "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" >>>>>> "--fixed_Gaussian"' returned non-zero exit status 135. >>>>>> >>>>>> ############################################### >>>>>> >>>>>> What is wrong? What would be the best way for doing so? I want to >>>>>> use this volume to finally make a soft mask in relion.... >>>>>> >>>>>> Thanks a lot, best, Dieter >>>>>> >>>>>> >>>>>> ################################################### >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> Dieter Blaas, >>>>>> Max Perutz Laboratories >>>>>> Medical University of Vienna, >>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>>>>> Dr. Bohr Gasse 9/3, >>>>>> A-1030 Vienna, Austria, >>>>>> Tel: 0043 1 4277 61630, >>>>>> Mobile: 0043 699 1942 1659 >>>>>> e-mail: die...@me... >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@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 >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@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 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dieter B. <die...@me...> - 2021-02-24 19:24:21
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Thank you all, good to know :-) just to add: What might be the reason for the error (see below for my original post)? best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: die...@me... ------------------------------------------------------------------------ On 24.02.2021 19:41, Carlos Oscar Sorzano wrote: > > Dear all, > > I totally agree. The most convenient way to create these volumes is > through the protocol. > > Cheers, Carlos Oscar > > On 2/24/21 4:31 PM, Pablo Conesa wrote: >> >> Hi Dieter, people from xmipp team is reading this list. So is the >> right email to be used. Although maybe a xmipp specific email could >> be more clearer. >> >> My line was, more than a clarification for you, a call for xmipp team >> to come to the rescue!. Which Carlos Oscar did. >> >> The way you used xmipp through scipion is fine. You could even do it >> in one line: >> >> *scipion3 **xmipp_volume_from_pdb* >> >> scipion3 will redirect command starting with "xmipp_*" to xmipp , >> "e2" or "sx" to eman, and "relion" to relion. >> >> I do not know a better way from the command line, unless you want to >> avoid scipion and use directly xmipp. There is a way, but then you >> need to install xmipp on its own, which might be more complex. >> >> The other way would be using scipion itself, you have a protocol for >> that, that its calling xmipp program in the backgound: >> >> >> On 24/2/21 13:30, Dieter Blaas wrote: >>> >>> Hi Pablo, >>> >>> thanks! I thought that this list was the successor of the xmipp >>> list. Sorry! >>> >>> Actually, I created the scipion3 environment with " conda activate >>> scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am >>> not sure whether this makes sense as I have been using the old >>> fashioned command line xmipp commands until I recently had to move >>> to scipion. >>> >>> I was wondering whether there was a better way of getting from pdb >>> files to volume files to be used as a starting map for relion >>> refinements or making masks etc. In fact, I appended a number of pdb >>> files and removed everything not being a coordinate. This file I >>> then tried to use for making a volume including all atoms.... >>> >>> best, Dieter >>> >>> ------------------------------------------------------------------------ >>> Dieter Blaas, >>> Max Perutz Laboratories >>> Medical University of Vienna, >>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>> Dr. Bohr Gasse 9/3, >>> A-1030 Vienna, Austria, >>> Tel: 0043 1 4277 61630, >>> Mobile: 0043 699 1942 1659 >>> e-mail:die...@me... >>> ------------------------------------------------------------------------ >>> On 23.02.2021 12:37, Pablo Conesa wrote: >>>> >>>> Hi Dieter! >>>> >>>> I think xmipp team should know more about the current status. >>>> >>>> One question, how are you invoking the xmipp command, though >>>> scipion3?, like scipion3 run xmipp_volume_from_pdb >>>> >>>> On 18/2/21 19:20, Dieter Blaas wrote: >>>>> Hi, >>>>> >>>>> I am trying to make a kind of mean volume from many aligned pdb >>>>> files. I appended all the pdbs and removed everything that is not >>>>> a coordinate record. This file I feed into xmipp like so: >>>>> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" >>>>> "--blobs" "--fixed_Gaussian". I am using an old version of this >>>>> script but I believe that it has not have changed over the years. >>>>> I get this: >>>>> >>>>> ############################################ >>>>> >>>>> PDB file: all_atoms.pdb >>>>> >>>>> Sampling rate: 1 >>>>> High sampling rate: 0.0833333 >>>>> Size: -1 >>>>> Center PDB: 0 >>>>> Do not Hetatm: 0 >>>>> Use blobs: 1 >>>>> Use poor Gaussian: 0 >>>>> Use fixed Gaussian: 1 >>>>> Intensity Col: occupancy >>>>> Sigma: -1 >>>>> >>>>> Bus error (core dumped) >>>>> Traceback (most recent call last): >>>>> File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", >>>>> line 8, in <module> >>>>> sys.exit(main()) >>>>> File >>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >>>>> line 43, in main >>>>> runProgram(program, params) >>>>> File >>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >>>>> line 64, in runProgram >>>>> pwutils.runJob(None, program, params, env=env) >>>>> File >>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>>> line 51, in runJob >>>>> return runCommand(command, env, cwd) >>>>> File >>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>>> line 66, in runCommand >>>>> check_call(command, shell=True, stdout=sys.stdout, >>>>> stderr=sys.stderr, >>>>> File >>>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >>>>> line 364, in check_call >>>>> raise CalledProcessError(retcode, cmd) >>>>> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" >>>>> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' >>>>> returned non-zero exit status 135. >>>>> >>>>> ############################################### >>>>> >>>>> What is wrong? What would be the best way for doing so? I want to >>>>> use this volume to finally make a soft mask in relion.... >>>>> >>>>> Thanks a lot, best, Dieter >>>>> >>>>> >>>>> ################################################### >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> Dieter Blaas, >>>>> Max Perutz Laboratories >>>>> Medical University of Vienna, >>>>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>>>> Dr. Bohr Gasse 9/3, >>>>> A-1030 Vienna, Austria, >>>>> Tel: 0043 1 4277 61630, >>>>> Mobile: 0043 699 1942 1659 >>>>> e-mail: die...@me... >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@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 >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Carlos O. S. <co...@cn...> - 2021-02-24 18:41:52
|
Dear all, I totally agree. The most convenient way to create these volumes is through the protocol. Cheers, Carlos Oscar On 2/24/21 4:31 PM, Pablo Conesa wrote: > > Hi Dieter, people from xmipp team is reading this list. So is the > right email to be used. Although maybe a xmipp specific email could be > more clearer. > > My line was, more than a clarification for you, a call for xmipp team > to come to the rescue!. Which Carlos Oscar did. > > The way you used xmipp through scipion is fine. You could even do it > in one line: > > *scipion3 **xmipp_volume_from_pdb* > > scipion3 will redirect command starting with "xmipp_*" to xmipp , "e2" > or "sx" to eman, and "relion" to relion. > > I do not know a better way from the command line, unless you want to > avoid scipion and use directly xmipp. There is a way, but then you > need to install xmipp on its own, which might be more complex. > > The other way would be using scipion itself, you have a protocol for > that, that its calling xmipp program in the backgound: > > > On 24/2/21 13:30, Dieter Blaas wrote: >> >> Hi Pablo, >> >> thanks! I thought that this list was the successor of the xmipp >> list. Sorry! >> >> Actually, I created the scipion3 environment with " conda activate >> scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am >> not sure whether this makes sense as I have been using the old >> fashioned command line xmipp commands until I recently had to move to >> scipion. >> >> I was wondering whether there was a better way of getting from pdb >> files to volume files to be used as a starting map for relion >> refinements or making masks etc. In fact, I appended a number of pdb >> files and removed everything not being a coordinate. This file I then >> tried to use for making a volume including all atoms.... >> >> best, Dieter >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Mobile: 0043 699 1942 1659 >> e-mail:die...@me... >> ------------------------------------------------------------------------ >> On 23.02.2021 12:37, Pablo Conesa wrote: >>> >>> Hi Dieter! >>> >>> I think xmipp team should know more about the current status. >>> >>> One question, how are you invoking the xmipp command, though >>> scipion3?, like scipion3 run xmipp_volume_from_pdb >>> >>> On 18/2/21 19:20, Dieter Blaas wrote: >>>> Hi, >>>> >>>> I am trying to make a kind of mean volume from many aligned pdb >>>> files. I appended all the pdbs and removed everything that is not a >>>> coordinate record. This file I feed into xmipp like so: >>>> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" >>>> "--blobs" "--fixed_Gaussian". I am using an old version of this >>>> script but I believe that it has not have changed over the years. I >>>> get this: >>>> >>>> ############################################ >>>> >>>> PDB file: all_atoms.pdb >>>> >>>> Sampling rate: 1 >>>> High sampling rate: 0.0833333 >>>> Size: -1 >>>> Center PDB: 0 >>>> Do not Hetatm: 0 >>>> Use blobs: 1 >>>> Use poor Gaussian: 0 >>>> Use fixed Gaussian: 1 >>>> Intensity Col: occupancy >>>> Sigma: -1 >>>> >>>> Bus error (core dumped) >>>> Traceback (most recent call last): >>>> File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", >>>> line 8, in <module> >>>> sys.exit(main()) >>>> File >>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >>>> line 43, in main >>>> runProgram(program, params) >>>> File >>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >>>> line 64, in runProgram >>>> pwutils.runJob(None, program, params, env=env) >>>> File >>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>> line 51, in runJob >>>> return runCommand(command, env, cwd) >>>> File >>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>>> line 66, in runCommand >>>> check_call(command, shell=True, stdout=sys.stdout, >>>> stderr=sys.stderr, >>>> File >>>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >>>> line 364, in check_call >>>> raise CalledProcessError(retcode, cmd) >>>> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" >>>> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' >>>> returned non-zero exit status 135. >>>> >>>> ############################################### >>>> >>>> What is wrong? What would be the best way for doing so? I want to >>>> use this volume to finally make a soft mask in relion.... >>>> >>>> Thanks a lot, best, Dieter >>>> >>>> >>>> ################################################### >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> Dieter Blaas, >>>> Max Perutz Laboratories >>>> Medical University of Vienna, >>>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>>> Dr. Bohr Gasse 9/3, >>>> A-1030 Vienna, Austria, >>>> Tel: 0043 1 4277 61630, >>>> Mobile: 0043 699 1942 1659 >>>> e-mail: die...@me... >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@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 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@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...> - 2021-02-24 15:47:07
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Dear Ana,
This is a bug in xmipp plugin, caused by a recent update of scipion (so
is more scipion fault). Xmipp team is already testing a fix and soon
will be released.
As a temporary hack, you can create the missing "tmp" folder at:
Runs/001218_XmippProtDeepMicrographScreen/*tmp*
**
On 23/2/21 9:17, Ana Andreea ARTENI wrote:
> Morning,
>
> When using deep micrograph cleaner/analyse results/: when placing the value 0.97 in the program and clicking on the "eye" nothing happens but in the terminal I get the following error:
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/tkinter/__init__.py", line 1883, in __call__
> return self.func(*args)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/gui/form.py", line 1281, in _visualizeVar
> self.visualizeCallback(self.paramName)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/viewer.py", line 265, in _visualizeParam
> views = self._getVisualizeDict()[paramName](paramName)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/viewers/viewer_deep_micrograph_cleaner.py", line 83, in _visualizeCoordinates
> newOutput = SetOfCoordinates(filename=coordsViewerFn)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pwem/objects/data.py", line 1437, in __init__
> EMSet.__init__(self, **kwargs)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1096, in __init__
> self.load()
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/object.py", line 1196, in load
> self._mapper = self._MapperClass(fn, self._loadClassesDict(), prefix, self._indexes)
> File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/mapper/sqlite.py", line 751, in __init__
> raise SqliteFlatMapperException('Error creating SqliteFlatMapper, '
> pyworkflow.mapper.sqlite.SqliteFlatMapperException: Error creating SqliteFlatMapper, dbName: Runs/001218_XmippProtDeepMicrographScreen/tmp/coordsViewer.sqlite, tablePrefix:
> error: unable to open database file
>
> How I can fix this?
> My kind regards,
> ana arteni.
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Pablo C. <pc...@cn...> - 2021-02-24 15:31:31
|
Hi Dieter, people from xmipp team is reading this list. So is the right email to be used. Although maybe a xmipp specific email could be more clearer. My line was, more than a clarification for you, a call for xmipp team to come to the rescue!. Which Carlos Oscar did. The way you used xmipp through scipion is fine. You could even do it in one line: *scipion3 **xmipp_volume_from_pdb* scipion3 will redirect command starting with "xmipp_*" to xmipp , "e2" or "sx" to eman, and "relion" to relion. I do not know a better way from the command line, unless you want to avoid scipion and use directly xmipp. There is a way, but then you need to install xmipp on its own, which might be more complex. The other way would be using scipion itself, you have a protocol for that, that its calling xmipp program in the backgound: ** On 24/2/21 13:30, Dieter Blaas wrote: > > Hi Pablo, > > thanks! I thought that this list was the successor of the xmipp > list. Sorry! > > Actually, I created the scipion3 environment with " conda activate > scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am > not sure whether this makes sense as I have been using the old > fashioned command line xmipp commands until I recently had to move to > scipion. > > I was wondering whether there was a better way of getting from pdb > files to volume files to be used as a starting map for relion > refinements or making masks etc. In fact, I appended a number of pdb > files and removed everything not being a coordinate. This file I then > tried to use for making a volume including all atoms.... > > best, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Mobile: 0043 699 1942 1659 > e-mail:die...@me... > ------------------------------------------------------------------------ > On 23.02.2021 12:37, Pablo Conesa wrote: >> >> Hi Dieter! >> >> I think xmipp team should know more about the current status. >> >> One question, how are you invoking the xmipp command, though >> scipion3?, like scipion3 run xmipp_volume_from_pdb >> >> On 18/2/21 19:20, Dieter Blaas wrote: >>> Hi, >>> >>> I am trying to make a kind of mean volume from many aligned pdb >>> files. I appended all the pdbs and removed everything that is not a >>> coordinate record. This file I feed into xmipp like so: >>> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" >>> "--fixed_Gaussian". I am using an old version of this script but I >>> believe that it has not have changed over the years. I get this: >>> >>> ############################################ >>> >>> PDB file: all_atoms.pdb >>> >>> Sampling rate: 1 >>> High sampling rate: 0.0833333 >>> Size: -1 >>> Center PDB: 0 >>> Do not Hetatm: 0 >>> Use blobs: 1 >>> Use poor Gaussian: 0 >>> Use fixed Gaussian: 1 >>> Intensity Col: occupancy >>> Sigma: -1 >>> >>> Bus error (core dumped) >>> Traceback (most recent call last): >>> File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", >>> line 8, in <module> >>> sys.exit(main()) >>> File >>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >>> line 43, in main >>> runProgram(program, params) >>> File >>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >>> line 64, in runProgram >>> pwutils.runJob(None, program, params, env=env) >>> File >>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>> line 51, in runJob >>> return runCommand(command, env, cwd) >>> File >>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >>> line 66, in runCommand >>> check_call(command, shell=True, stdout=sys.stdout, >>> stderr=sys.stderr, >>> File >>> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >>> line 364, in check_call >>> raise CalledProcessError(retcode, cmd) >>> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" >>> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' >>> returned non-zero exit status 135. >>> >>> ############################################### >>> >>> What is wrong? What would be the best way for doing so? I want to >>> use this volume to finally make a soft mask in relion.... >>> >>> Thanks a lot, best, Dieter >>> >>> >>> ################################################### >>> >>> ------------------------------------------------------------------------ >>> >>> Dieter Blaas, >>> Max Perutz Laboratories >>> Medical University of Vienna, >>> Inst. Med. Biochem., Vienna Biocenter (VBC), >>> Dr. Bohr Gasse 9/3, >>> A-1030 Vienna, Austria, >>> Tel: 0043 1 4277 61630, >>> Mobile: 0043 699 1942 1659 >>> e-mail: die...@me... >>> ------------------------------------------------------------------------ >>> >>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@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 > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Dieter B. <die...@me...> - 2021-02-24 12:31:03
|
Hi Pablo, thanks! I thought that this list was the successor of the xmipp list. Sorry! Actually, I created the scipion3 environment with " conda activate scipion3" and invoked it with "scipion xmipp_volume_from_pdb". I am not sure whether this makes sense as I have been using the old fashioned command line xmipp commands until I recently had to move to scipion. I was wondering whether there was a better way of getting from pdb files to volume files to be used as a starting map for relion refinements or making masks etc. In fact, I appended a number of pdb files and removed everything not being a coordinate. This file I then tried to use for making a volume including all atoms.... best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: die...@me... ------------------------------------------------------------------------ On 23.02.2021 12:37, Pablo Conesa wrote: > > Hi Dieter! > > I think xmipp team should know more about the current status. > > One question, how are you invoking the xmipp command, though > scipion3?, like scipion3 run xmipp_volume_from_pdb > > On 18/2/21 19:20, Dieter Blaas wrote: >> Hi, >> >> I am trying to make a kind of mean volume from many aligned pdb >> files. I appended all the pdbs and removed everything that is not a >> coordinate record. This file I feed into xmipp like so: >> xmipp_volume_from_pdb "-i" "all_atoms.pdb" "-o" "all_test" "--blobs" >> "--fixed_Gaussian". I am using an old version of this script but I >> believe that it has not have changed over the years. I get this: >> >> ############################################ >> >> PDB file: all_atoms.pdb >> >> Sampling rate: 1 >> High sampling rate: 0.0833333 >> Size: -1 >> Center PDB: 0 >> Do not Hetatm: 0 >> Use blobs: 1 >> Use poor Gaussian: 0 >> Use fixed Gaussian: 1 >> Intensity Col: occupancy >> Sigma: -1 >> >> Bus error (core dumped) >> Traceback (most recent call last): >> File "/home/blaas/.local/anaconda3/envs/scipion3/bin/emprogram", >> line 8, in <module> >> sys.exit(main()) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/cmd/program.py", >> line 43, in main >> runProgram(program, params) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pwem/utils.py", >> line 64, in runProgram >> pwutils.runJob(None, program, params, env=env) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >> line 51, in runJob >> return runCommand(command, env, cwd) >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", >> line 66, in runCommand >> check_call(command, shell=True, stdout=sys.stdout, >> stderr=sys.stderr, >> File >> "/home/blaas/.local/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", >> line 364, in check_call >> raise CalledProcessError(retcode, cmd) >> subprocess.CalledProcessError: Command 'xmipp_volume_from_pdb "-i" >> "all_atoms.pdb" "-o" "all_test" "--blobs" "--fixed_Gaussian"' >> returned non-zero exit status 135. >> >> ############################################### >> >> What is wrong? What would be the best way for doing so? I want to use >> this volume to finally make a soft mask in relion.... >> >> Thanks a lot, best, Dieter >> >> >> ################################################### >> >> ------------------------------------------------------------------------ >> Dieter Blaas, >> Max Perutz Laboratories >> Medical University of Vienna, >> Inst. Med. Biochem., Vienna Biocenter (VBC), >> Dr. Bohr Gasse 9/3, >> A-1030 Vienna, Austria, >> Tel: 0043 1 4277 61630, >> Mobile: 0043 699 1942 1659 >> e-mail: die...@me... >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@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 |
|
From: Pablo C. <pc...@cn...> - 2021-02-24 10:01:28
|
Dear all, tomography plugins are still unstable. I have temporarily hide them form the plugin manger to avoid installing them. We are very happy how it is all coming together and most of the basic tomography pipeline is being covered with Imod, Dynamo, Eman, Xmipp, MC2, gCTF, NovaCTF, pyseg, deepfinder, relion, cryoCARE, jjSoft... But still not usable under our supervision. I'd say we are somewhere in an alpha state....getting closer to a beta. Once we feel is stable enough for betatesting, I'll announce it and everyone is very welcome to betatest the tomography functionality. On 24/2/21 8:48, Ana Andreea ARTENI wrote: > Morning, > I also have errors for reliontomo: > > Scipion v3.0.7 - Eugenius > WARNING FOR DEVELOPERS: phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough. > > error when importing from reliontomo.protocols: cannot import name 'pwem' from 'relion.convert' (/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/convert/__init__.py) > File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > My kind regards, > ana arteni. > > ----- Original Message ----- > From: "scipion-users" <sci...@li...> > To: "scipion-users" <sci...@li...> > Cc: "Hoover, David (NIH/CIT) [E]" <hoo...@hp...> > Sent: Wednesday, 24 February, 2021 03:02:43 > Subject: [scipion-users] Error with reliontomo tests > > Hi, > > I've managed to install scipion3 (3.0.7) and am trying to run tests. The reliontomo test doesn't seem to work at all: > > ================================================================================================================ > > $ scipion3 tests --show > > ... >>>>> reliontomo > Error loading the test. Please, run the test for more information: reliontomo.tests.test_workflow_reliontomo > ... > > $ scipion3 tests reliontomo.tests.test_workflow_reliontomo > Scipion v3.0.7 - Eugenius > Running tests.... > WARNING FOR DEVELOPERS: phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough. > [ FAILED ] _FailedTest.test_workflow_reliontomo > > Traceback (most recent call last): > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor > yield > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run > self._callTestMethod(testMethod) > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod > method() > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 34, in testFailure > raise self._exception > ImportError: Failed to import test module: test_workflow_reliontomo > Traceback (most recent call last): > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName > module = __import__(module_name) > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/tests/test_workflow_reliontomo.py", line 35, in <module> > from reliontomo.protocols.protocol_ctf_3d_estimation import CTF3D_PER_SUBVOLUME > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/__init__.py", line 28, in <module> > from .protocol_refine_3d_tomo import ProtRelionSubtomoRefine3D > File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module> > from relion.convert import Table, pwem, convert31 > ImportError: cannot import name 'pwem' from 'relion.convert' (/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/__init__.py) > > > [==========] run 1 tests (0.001 secs) > [ FAILED ] 1 tests > [ PASSED ] 0 tests > > ================================================================================================================ > > Is there something I am missing? > > David -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: David <dst...@cn...> - 2021-02-24 08:28:37
|
Hi David, recommended approach is to use HDF5 distributed via standard channels, e.g. via apt on Ubuntu machines: sudo apt install libhdf5-dev Other tested option is to install it via conda in your virtual environment, provided you use it (as written already by David M.): activate your Scipion's conda environment and, then: conda install hdf5 -y -c defaults On Ubuntu 20.04LTS, apt will fetch version /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103.0.0 (as written by Pablo). It indeed seems to be version 1.10.4 (https://packages.ubuntu.com/focal/libhdf5-103), though I have to admit that I'm lost in this versioning name convention. Conda will fetch version 1.12, which goes to libhdf5_cpp.so.200.0.0 I have no experience with locally compiled version. You should not see any compilation errors (related to HDF5 or not) :) Based on your compiler and Cuda version, you might see some compilation warnings though. Hope this helps. If your problem persist, let us know and we can schedule a call. KR, David Strelak > > ---------- Původní e-mail ---------- > Od: Carlos Oscar Sorzano <co...@cn...> > Komu: Pablo Conesa <pc...@cn...>, hoo...@hp..., > Mailing list for Scipion users <sci...@li...>, > David Střelák <Dav...@se...> > Datum: 23. 2. 2021 20:20:18 > Předmět: Re: Fwd: Re: [scipion-users] make externally compiled HDF5 > available for xmipp compile > > > Dear David, > > this compilation issue really goes out of my expertise. Which are > the compilation errors you see? If they are solved by using > different functions from Xmipp, we may try to solve them. If you > want, we could have a separate call to see these errors in detail. > > Kind regards, Carlos Oscar > > On 2/23/21 12:40 PM, Pablo Conesa wrote: > > > > -------- Forwarded Message -------- > Subject: Re: [scipion-users] make externally compiled HDF5 > available for xmipp compile > Date: Fri, 19 Feb 2021 11:22:13 -0500 > From: Hoover, David (NIH/CIT) [E] via scipion-users > <sci...@li...> > <mailto:sci...@li...> > Reply-To: Mailing list for Scipion users > <sci...@li...> > <mailto:sci...@li...> > To: sci...@li... > <mailto:sci...@li...> > CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...> > <mailto:hoo...@hp...> > > > > Was it compiled with 1.8.x API compatibility macros? I am > seeing errors unless I compile HDF5 with > --with-default-api-version=v18 option. > > https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html > > David > > On 2/19/2021 9:43 AM, Pablo Conesa wrote: > > Mine is linked to : > > libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 > (0x00007f354a368000) > libhdf5_cpp.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 > (0x00007f354a2eb000) > > I think is 1.10.4 > > On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via > scipion-users wrote: > > One more question: what version of HDF5 does xmipp > require? > > David > > On 2/19/2021 2:26 AM, Pablo Conesa wrote: > > Thanks Jason. > > There is a detailed "custom xmipp installation" > page > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > where you can adapt xmipp to your system, > providing default installation does not work. > > > On 19/2/21 1:13, Jason Key wrote: > > Hi David, > > On Thu, Feb 18, 2021 at 12:42 PM Hoover, David > (NIH/CIT) [E] via > scipion-users<sci...@li...> > <mailto:sci...@li...> > wrote: > > Is there any way of making HDF5 headers > and libraries available for compiling xmipp? > That is, must I install HDF5 with yum or > apt-get into /usr/lib and /usr/include, or > is there an environment variable or > configuration setting that can be set to > force the compile to look elsewhere for > the header and library files? > > I was able to do this by adding INCDIRFLAGS > and LIBDIRFLAGS variables > to the xmipp.conf file in > "software/em/xmippSrc-v3.20.07". > > Best, > Jason > > -- Pablo Conesa - *Madrid Scipion > <http://scipion.i2pc.es> <http://scipion.i2pc.es> > team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> > <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > -- > David Hoover, Ph.D. > Computational Biologist > High Performance Computing Services, > Center for Information Technology, > National Institutes of Health > 12 South Dr., Rm 2N207 > Bethesda, MD 20892, USA > TEL: (+1) 301-435-2986 > Email:hoo...@hp... <mailto:hoo...@hp...> > > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Ana A. A. <ana...@i2...> - 2021-02-24 08:07:20
|
Morning,
I also have errors for reliontomo:
Scipion v3.0.7 - Eugenius
WARNING FOR DEVELOPERS: phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough.
> error when importing from reliontomo.protocols: cannot import name 'pwem' from 'relion.convert' (/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/convert/__init__.py)
File "/home/anne-pascale.jaudier/.conda/envs/.scipion3env/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module>
Check the plugin manager (Configuration->Plugins in Scipion manager window)
or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades,
it could be a versions compatibility issue.
My kind regards,
ana arteni.
----- Original Message -----
From: "scipion-users" <sci...@li...>
To: "scipion-users" <sci...@li...>
Cc: "Hoover, David (NIH/CIT) [E]" <hoo...@hp...>
Sent: Wednesday, 24 February, 2021 03:02:43
Subject: [scipion-users] Error with reliontomo tests
Hi,
I've managed to install scipion3 (3.0.7) and am trying to run tests. The reliontomo test doesn't seem to work at all:
================================================================================================================
$ scipion3 tests --show
...
>>>> reliontomo
Error loading the test. Please, run the test for more information: reliontomo.tests.test_workflow_reliontomo
...
$ scipion3 tests reliontomo.tests.test_workflow_reliontomo
Scipion v3.0.7 - Eugenius
Running tests....
WARNING FOR DEVELOPERS: phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough.
[ FAILED ] _FailedTest.test_workflow_reliontomo
Traceback (most recent call last):
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
yield
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
self._callTestMethod(testMethod)
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
method()
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 34, in testFailure
raise self._exception
ImportError: Failed to import test module: test_workflow_reliontomo
Traceback (most recent call last):
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/tests/test_workflow_reliontomo.py", line 35, in <module>
from reliontomo.protocols.protocol_ctf_3d_estimation import CTF3D_PER_SUBVOLUME
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/__init__.py", line 28, in <module>
from .protocol_refine_3d_tomo import ProtRelionSubtomoRefine3D
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module>
from relion.convert import Table, pwem, convert31
ImportError: cannot import name 'pwem' from 'relion.convert' (/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/__init__.py)
[==========] run 1 tests (0.001 secs)
[ FAILED ] 1 tests
[ PASSED ] 0 tests
================================================================================================================
Is there something I am missing?
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoo...@hp...
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scipion-users mailing list
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https://lists.sourceforge.net/lists/listinfo/scipion-users
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From: David M. <dma...@ub...> - 2021-02-24 06:06:01
|
Hi there, Just to explore another possibility, if you didn't try it yet. If you installed Scipion/Xmipp under conda, there is the chance to install hdf5 via conda. It's just to activate the Scipion's conda environment and, then 'conda install hdf5 -y -c defaults'. Xmipp tries to install it in this way when hdf5 is not found in the system. Perhaps, in your case, that installation was not triggered because Xmipp found a hdf5 installation in the system, even though it's making incompatibilities. I hope it will help. Cheers, <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, Feb 23, 2021 at 8:55 PM Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li...<mailto:sci...@li...>> wrote: Unfortunately, I did not save the errors, but they were indicative of an misunderstood API call. Bottom line, xmipp requires 1.8.x API; our local install of HDF5 v1.10.x or v1.6.x broke the xmipp compilation. That's my burden of hosting a spectrum of versions for every library and application. I assume you all don't see this because HDF5 comes from a standard yum or apt-get package. David On 2/23/2021 2:17 PM, Carlos Oscar Sorzano wrote: > Dear David, > > this compilation issue really goes out of my expertise. Which are the compilation errors you see? If they are solved by using different functions from Xmipp, we may try to solve them. If you want, we could have a separate call to see these errors in detail. > > Kind regards, Carlos Oscar > > On 2/23/21 12:40 PM, Pablo Conesa wrote: >> >> >> -------- Forwarded Message -------- >> Subject: Re: [scipion-users] make externally compiled HDF5 available for xmipp compile >> Date: Fri, 19 Feb 2021 11:22:13 -0500 >> From: Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li...<mailto:sci...@li...>> >> Reply-To: Mailing list for Scipion users <sci...@li...<mailto:sci...@li...>> >> To: sci...@li...<mailto:sci...@li...> >> CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...<mailto:hoo...@hp...>> >> >> >> >> Was it compiled with 1.8.x API compatibility macros? I am seeing errors unless I compile HDF5 with --with-default-api-version=v18 option. >> >> https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html >> >> David >> >> On 2/19/2021 9:43 AM, Pablo Conesa wrote: >>> Mine is linked to : >>> >>> libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) >>> libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000) >>> >>> I think is 1.10.4 >>> >>> On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >>>> One more question: what version of HDF5 does xmipp require? >>>> >>>> David >>>> >>>> On 2/19/2021 2:26 AM, Pablo Conesa wrote: >>>>> Thanks Jason. >>>>> >>>>> There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work. >>>>> >>>>> >>>>> On 19/2/21 1:13, Jason Key wrote: >>>>>> Hi David, >>>>>> >>>>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >>>>>> scipion-users<sci...@li...<mailto:sci...@li...>> wrote: >>>>>>> Is there any way of making HDF5 headers and libraries available for compiling xmipp? >>>>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? >>>>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >>>>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >>>>>> >>>>>> Best, >>>>>> Jason >>>>>> >>>>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li...<mailto:sci...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li...<mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> -- >> David Hoover, Ph.D. >> Computational Biologist >> High Performance Computing Services, >> Center for Information Technology, >> National Institutes of Health >> 12 South Dr., Rm 2N207 >> Bethesda, MD 20892, USA >> TEL: (+1) 301-435-2986 >> Email:hoo...@hp...<mailto:Email%3Ah...@hp...> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li...<mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp...<mailto:hoo...@hp...> _______________________________________________ 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. 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: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2021-02-24 02:03:09
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Hi,
I've managed to install scipion3 (3.0.7) and am trying to run tests. The reliontomo test doesn't seem to work at all:
================================================================================================================
$ scipion3 tests --show
...
>>>> reliontomo
Error loading the test. Please, run the test for more information: reliontomo.tests.test_workflow_reliontomo
...
$ scipion3 tests reliontomo.tests.test_workflow_reliontomo
Scipion v3.0.7 - Eugenius
Running tests....
WARNING FOR DEVELOPERS: phenix/bibtex._bibtex unnecessarily declared. Just the doc string is enough.
[ FAILED ] _FailedTest.test_workflow_reliontomo
Traceback (most recent call last):
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
yield
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
self._callTestMethod(testMethod)
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
method()
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 34, in testFailure
raise self._exception
ImportError: Failed to import test module: test_workflow_reliontomo
Traceback (most recent call last):
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/unittest/loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/tests/test_workflow_reliontomo.py", line 35, in <module>
from reliontomo.protocols.protocol_ctf_3d_estimation import CTF3D_PER_SUBVOLUME
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/__init__.py", line 28, in <module>
from .protocol_refine_3d_tomo import ProtRelionSubtomoRefine3D
File "/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/reliontomo/protocols/protocol_refine_3d_tomo.py", line 34, in <module>
from relion.convert import Table, pwem, convert31
ImportError: cannot import name 'pwem' from 'relion.convert' (/usr/local/apps/scipion/3.0.7/anaconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/__init__.py)
[==========] run 1 tests (0.001 secs)
[ FAILED ] 1 tests
[ PASSED ] 0 tests
================================================================================================================
Is there something I am missing?
David
--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoo...@hp...
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From: David M. <dma...@gm...> - 2021-02-24 00:36:49
|
Hi there, Just to explore another possibility, if you didn't try it yet. If you installed Scipion/Xmipp under conda, there is the chance to install hdf5 via conda. It's just to activate the Scipion's conda environ and, then 'conda install hdf5 -y -c defaults'. Xmipp tries to install it in this way when hdf5 is not found in the system. Perhaps, in your case that installation was not triggered because Xmipp found a hdf5 installation in the system, even it's making incompatibilities. I hope it will helps. Cheers, _____ Dr. David Maluenda Niubó (+34) 619.029.310 - dma...@ub... Wavefront Engineering Group Applied Physics (UB) El mar., 23 feb. 2021 20:55, Hoover, David (NIH/CIT) [E] via scipion-users < sci...@li...> escribió: > Unfortunately, I did not save the errors, but they were indicative of an > misunderstood API call. Bottom line, xmipp requires 1.8.x API; our local > install of HDF5 v1.10.x or v1.6.x broke the xmipp compilation. That's my > burden of hosting a spectrum of versions for every library and > application. I assume you all don't see this because HDF5 comes from a > standard yum or apt-get package. > > David > > On 2/23/2021 2:17 PM, Carlos Oscar Sorzano wrote: > > Dear David, > > > > this compilation issue really goes out of my expertise. Which are the > compilation errors you see? If they are solved by using different functions > from Xmipp, we may try to solve them. If you want, we could have a separate > call to see these errors in detail. > > > > Kind regards, Carlos Oscar > > > > On 2/23/21 12:40 PM, Pablo Conesa wrote: > >> > >> > >> -------- Forwarded Message -------- > >> Subject: Re: [scipion-users] make externally compiled HDF5 > available for xmipp compile > >> Date: Fri, 19 Feb 2021 11:22:13 -0500 > >> From: Hoover, David (NIH/CIT) [E] via scipion-users < > sci...@li...> > >> Reply-To: Mailing list for Scipion users < > sci...@li...> > >> To: sci...@li... > >> CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...> > >> > >> > >> > >> Was it compiled with 1.8.x API compatibility macros? I am seeing errors > unless I compile HDF5 with --with-default-api-version=v18 option. > >> > >> https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html > >> > >> David > >> > >> On 2/19/2021 9:43 AM, Pablo Conesa wrote: > >>> Mine is linked to : > >>> > >>> libhdf5_serial.so.103 => > /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) > >>> libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 > (0x00007f354a2eb000) > >>> > >>> I think is 1.10.4 > >>> > >>> On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: > >>>> One more question: what version of HDF5 does xmipp require? > >>>> > >>>> David > >>>> > >>>> On 2/19/2021 2:26 AM, Pablo Conesa wrote: > >>>>> Thanks Jason. > >>>>> > >>>>> There is a detailed "custom xmipp installation" page < > https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> > where you can adapt xmipp to your system, providing default installation > does not work. > >>>>> > >>>>> > >>>>> On 19/2/21 1:13, Jason Key wrote: > >>>>>> Hi David, > >>>>>> > >>>>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via > >>>>>> scipion-users<sci...@li...> wrote: > >>>>>>> Is there any way of making HDF5 headers and libraries available > for compiling xmipp? > >>>>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and > /usr/include, or is there an environment variable or configuration setting > that can be set to force the compile to look elsewhere for the header and > library files? > >>>>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS > variables > >>>>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". > >>>>>> > >>>>>> Best, > >>>>>> Jason > >>>>>> > >>>>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> scipion-users mailing list > >>>>> sci...@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 > >>> > >> > >> -- > >> David Hoover, Ph.D. > >> Computational Biologist > >> High Performance Computing Services, > >> Center for Information Technology, > >> National Institutes of Health > >> 12 South Dr., Rm 2N207 > >> Bethesda, MD 20892, USA > >> TEL: (+1) 301-435-2986 > >> Email:hoo...@hp... > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > >> https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > David Hoover, Ph.D. > Computational Biologist > High Performance Computing Services, > Center for Information Technology, > National Institutes of Health > 12 South Dr., Rm 2N207 > Bethesda, MD 20892, USA > TEL: (+1) 301-435-2986 > Email: hoo...@hp... > > > _______________________________________________ > scipion-users mailing list > 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. > |
|
From: Hoover, D. (NIH/C. [E] <hoo...@hp...> - 2021-02-23 19:55:34
|
Unfortunately, I did not save the errors, but they were indicative of an misunderstood API call. Bottom line, xmipp requires 1.8.x API; our local install of HDF5 v1.10.x or v1.6.x broke the xmipp compilation. That's my burden of hosting a spectrum of versions for every library and application. I assume you all don't see this because HDF5 comes from a standard yum or apt-get package. David On 2/23/2021 2:17 PM, Carlos Oscar Sorzano wrote: > Dear David, > > this compilation issue really goes out of my expertise. Which are the compilation errors you see? If they are solved by using different functions from Xmipp, we may try to solve them. If you want, we could have a separate call to see these errors in detail. > > Kind regards, Carlos Oscar > > On 2/23/21 12:40 PM, Pablo Conesa wrote: >> >> >> -------- Forwarded Message -------- >> Subject: Re: [scipion-users] make externally compiled HDF5 available for xmipp compile >> Date: Fri, 19 Feb 2021 11:22:13 -0500 >> From: Hoover, David (NIH/CIT) [E] via scipion-users <sci...@li...> >> Reply-To: Mailing list for Scipion users <sci...@li...> >> To: sci...@li... >> CC: Hoover, David (NIH/CIT) [E] <hoo...@hp...> >> >> >> >> Was it compiled with 1.8.x API compatibility macros? I am seeing errors unless I compile HDF5 with --with-default-api-version=v18 option. >> >> https://support.hdfgroup.org/HDF5/doc/RM/APICompatMacros.html >> >> David >> >> On 2/19/2021 9:43 AM, Pablo Conesa wrote: >>> Mine is linked to : >>> >>> libhdf5_serial.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f354a368000) >>> libhdf5_cpp.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so.103 (0x00007f354a2eb000) >>> >>> I think is 1.10.4 >>> >>> On 19/2/21 14:31, Hoover, David (NIH/CIT) [E] via scipion-users wrote: >>>> One more question: what version of HDF5 does xmipp require? >>>> >>>> David >>>> >>>> On 2/19/2021 2:26 AM, Pablo Conesa wrote: >>>>> Thanks Jason. >>>>> >>>>> There is a detailed "custom xmipp installation" page <https://github.com/I2PC/xmipp/wiki/Xmipp-configuration-(version-20.07)> where you can adapt xmipp to your system, providing default installation does not work. >>>>> >>>>> >>>>> On 19/2/21 1:13, Jason Key wrote: >>>>>> Hi David, >>>>>> >>>>>> On Thu, Feb 18, 2021 at 12:42 PM Hoover, David (NIH/CIT) [E] via >>>>>> scipion-users<sci...@li...> wrote: >>>>>>> Is there any way of making HDF5 headers and libraries available for compiling xmipp? >>>>>>> That is, must I install HDF5 with yum or apt-get into /usr/lib and /usr/include, or is there an environment variable or configuration setting that can be set to force the compile to look elsewhere for the header and library files? >>>>>> I was able to do this by adding INCDIRFLAGS and LIBDIRFLAGS variables >>>>>> to the xmipp.conf file in "software/em/xmippSrc-v3.20.07". >>>>>> >>>>>> Best, >>>>>> Jason >>>>>> >>>>> -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@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 >>> >> >> -- >> David Hoover, Ph.D. >> Computational Biologist >> High Performance Computing Services, >> Center for Information Technology, >> National Institutes of Health >> 12 South Dr., Rm 2N207 >> Bethesda, MD 20892, USA >> TEL: (+1) 301-435-2986 >> Email:hoo...@hp... >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hoo...@hp... |
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