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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> |
