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Re: [scipion-users] micelle density subtraction
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From: Dmitry A. S. <sem...@gm...> - 2021-06-30 10:45:38
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span lang=EN-GB>Hello Roberto,<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 got his error while running the script<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 the <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Input 3D Map - was my 3D map<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Select the operation ot perform – Subtraction<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Subtractuin / Mask of – 3D map<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Map to subtract (subtrahend) – Masking volume<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>Any ideas?<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>P.s. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>When the program fails it doesn’t mark red.<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>Sincerely,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-GB>Dmitry<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><o:p> </o:p></span></p><p class=MsoNormal>File 'Runs/043619_ChimeraSubtractionMaps/logs/run.stdout' doesn't exist00001: RUNNING PROTOCOL -----------------</p><p class=MsoNormal>00002: Hostname: localhost4.localdomain4</p><p class=MsoNormal>00003: PID: 91697</p><p class=MsoNormal>00004: pyworkflow: 3.0.14</p><p class=MsoNormal>00005: plugin: chimerax</p><p class=MsoNormal>00006: plugin v: 3.0.5</p><p class=MsoNormal>00007: currentDir: /home/user/Data/ScipionUserData/projects/Colette__03_06__20</p><p class=MsoNormal>00008: workingDir: Runs/043619_ChimeraSubtractionMaps</p><p class=MsoNormal>00009: runMode: Restart</p><p class=MsoNormal>00010: MPI: 1</p><p class=MsoNormal>00011: threads: 1</p><p class=MsoNormal>00012: Starting at step: 1</p><p class=MsoNormal>00013: Running steps </p><p class=MsoNormal>00014: STARTED: prerequisitesStep, step 1, time 2021-06-30 12:40:02.645196</p><p class=MsoNormal>00015: Reference map:</p><p class=MsoNormal>00016: /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/042103_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P12_J63_010_volume_map.mrc</p><p class=MsoNormal>00017: </p><p class=MsoNormal>00018: Map to subtract:</p><p class=MsoNormal>00019: /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/041540_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine.mrc</p><p class=MsoNormal>00020: </p><p class=MsoNormal>00021: FINISHED: prerequisitesStep, step 1, time 2021-06-30 12:40:02.646980</p><p class=MsoNormal>00022: STARTED: runChimeraStep, step 2, time 2021-06-30 12:40:02.664428</p><p class=MsoNormal>00023: /bin/sh: /usr/bin/chimerax/bin/ChimeraX: Not a directory</p><p class=MsoNormal>00024: ** Running command: /usr/bin/chimerax/bin/ChimeraX --script /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc</p><p class=MsoNormal>00025: Traceback (most recent call last):</p><p class=MsoNormal>00026: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</p><p class=MsoNormal>00027: self._run()</p><p class=MsoNormal>00028: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</p><p class=MsoNormal>00029: resultFiles = self._runFunc()</p><p class=MsoNormal>00030: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</p><p class=MsoNormal>00031: return self._func(*self._args)</p><p class=MsoNormal>00032: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/chimera/protocols/protocol_subtraction_maps.py", line 583, in runChimeraStep</p><p class=MsoNormal>00033: Plugin.runChimeraProgram(Plugin.getProgram(), args, cwd=cwd, extraEnv=getEnvDictionary(self))</p><p class=MsoNormal>00034: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/chimera/__init__.py", line 66, in runChimeraProgram</p><p class=MsoNormal>00035: pwutils.runJob(None, program, args, env=env, cwd=cwd)</p><p class=MsoNormal>00036: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob</p><p class=MsoNormal>00037: return runCommand(command, env, cwd)</p><p class=MsoNormal>00038: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand</p><p class=MsoNormal>00039: check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,</p><p class=MsoNormal>00040: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call</p><p class=MsoNormal>00041: raise CalledProcessError(retcode, cmd)</p><p class=MsoNormal>00042: subprocess.CalledProcessError: Command ' /usr/bin/chimerax/bin/ChimeraX --script /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc' returned non-zero exit status 126.</p><p class=MsoNormal>00043: Protocol failed: Command ' /usr/bin/chimerax/bin/ChimeraX --script /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc' returned non-zero exit status 126.</p><p class=MsoNormal>00044: FAILED: runChimeraStep, step 2, time 2021-06-30 12:40:02.682864</p><p class=MsoNormal>00045: *** Last status is failed </p><p class=MsoNormal>00046: ------------------- PROTOCOL FAILED (DONE 2/3)</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:ro...@cn...">Roberto Marabini</a><br><b>Sent: </b>Wednesday, June 30, 2021 12:35 AM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] micelle density subtraction</p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Hi,</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> This is not a chimera function but a Scipion protocol.</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> cheers</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> </p></div><div><p class=MsoNormal> Roberto</p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Tue, Jun 29, 2021 at 6:07 PM Dmitry A. Semchonok <<a href="mailto:sem...@gm...">sem...@gm...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>Thank you, Roberto,</span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB> </span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-GB>I will investigate closer this function in chimera.</span></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div style='border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-color:currentcolor currentcolor'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:ro...@cn..." target="_blank">Roberto Marabini</a><br><b>Sent: </b>Tuesday, June 29, 2021 12:24 PM<br><b>To: </b><a href="mailto:sci...@li..." target="_blank">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] micelle density subtraction</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi,</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> Protocol "chimera-map subtraction" is an option but think first if you want to subtract or two mask the detergent micelle density (both options are available in the protocol)</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> Roberto</p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Tue, Jun 29, 2021 at 11:57 AM Dmitry A. Semchonok <<a href="mailto:sem...@gm..." target="_blank">sem...@gm...</a>> wrote:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid windowtext 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear colleagues,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>We need to subtract the detergent micelle density from the result 3D map.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>The idea to run the 3D refinement after the subtraction and with that improve the resolution.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>What are the ways to do that?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>(We currently have no model of my 3D map).</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you in advance.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sincerely,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dmitry</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
