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Re: [scipion-users] micelle density subtraction
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From: Roberto M. <ro...@cn...> - 2021-06-30 13:20:40
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Hi, The protocol executes the command: /usr/bin/chimerax/bin/ChimeraX --script /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc So, 1) open the file /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc with a text editor 2) Start chimerax (outside scipion), and copy and paste the commands in "chimeraScript.cxc" line by line. In this way, you can identify which is the command that fails. If the problem is that "scipionwrite command returns error: "Unkown command: scipionwrite"" then read https://github.com/scipion-em/scipion-em-chimera/blob/devel/FAQ.rst hope this helps. Roberto On Wed, Jun 30, 2021 at 12:45 PM Dmitry A. Semchonok <sem...@gm...> wrote: > Hello Roberto, > > > > I got his error while running the script > > > > So the > > Input 3D Map - was my 3D map > > Select the operation ot perform – Subtraction > > Subtractuin / Mask of – 3D map > > Map to subtract (subtrahend) – Masking volume > > > > Any ideas? > > > > P.s. > > When the program fails it doesn’t mark red. > > > > Sincerely, > > Dmitry > > > > > > > > File 'Runs/043619_ChimeraSubtractionMaps/logs/run.stdout' doesn't > exist00001: RUNNING PROTOCOL ----------------- > > 00002: Hostname: localhost4.localdomain4 > > 00003: PID: 91697 > > 00004: pyworkflow: 3.0.14 > > 00005: plugin: chimerax > > 00006: plugin v: 3.0.5 > > 00007: currentDir: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20 > > 00008: workingDir: Runs/043619_ChimeraSubtractionMaps > > 00009: runMode: Restart > > 00010: MPI: 1 > > 00011: threads: 1 > > 00012: Starting at step: 1 > > 00013: Running steps > > 00014: STARTED: prerequisitesStep, step 1, time 2021-06-30 > 12:40:02.645196 > > 00015: Reference map: > > 00016: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/042103_ProtCryoSparcNewNonUniformRefine3D/extra/cryosparc_P12_J63_010_volume_map.mrc > > 00017: > > 00018: Map to subtract: > > 00019: > /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/041540_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine.mrc > > 00020: > > 00021: FINISHED: prerequisitesStep, step 1, time 2021-06-30 > 12:40:02.646980 > > 00022: STARTED: runChimeraStep, step 2, time 2021-06-30 12:40:02.664428 > > 00023: /bin/sh: /usr/bin/chimerax/bin/ChimeraX: Not a directory > > 00024: ** Running command: /usr/bin/chimerax/bin/ChimeraX --script > /home/user/Data/ScipionUserData/projects/Colette__03_06__20/Runs/043619_ChimeraSubtractionMaps/tmp/chimeraScript.cxc > > 00025: Traceback (most recent call last): > > 00026: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 197, in run > > 00027: self._run() > > 00028: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 248, in _run > > 00029: resultFiles = self._runFunc() > > 00030: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", > line 244, in _runFunc > > 00031: return self._func(*self._args) > > 00032: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/chimera/protocols/protocol_subtraction_maps.py", > line 583, in runChimeraStep > > 00033: Plugin.runChimeraProgram(Plugin.getProgram(), args, cwd=cwd, > extraEnv=getEnvDictionary(self)) > > 00034: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/chimera/__init__.py", > line 66, in runChimeraProgram > > 00035: pwutils.runJob(None, program, args, env=env, cwd=cwd) > > 00036: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 52, in runJob > > 00037: return runCommand(command, env, cwd) > > 00038: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", > line 67, in runCommand > > 00039: check_call(command, shell=True, stdout=sys.stdout, > stderr=sys.stderr, > > 00040: File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", > line 364, in check_call > > 00041: raise CalledProcessError(retcode, cmd) > > 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. > > 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. > > 00044: FAILED: runChimeraStep, step 2, time 2021-06-30 12:40:02.682864 > > 00045: *** Last status is failed > > 00046: ------------------- PROTOCOL FAILED (DONE 2/3) > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Roberto Marabini <ro...@cn...> > *Sent: *Wednesday, June 30, 2021 12:35 AM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] micelle density subtraction > > > > Hi, > > > > This is not a chimera function but a Scipion protocol. > > > > cheers > > > > > > Roberto > > > > On Tue, Jun 29, 2021 at 6:07 PM Dmitry A. Semchonok <sem...@gm...> > wrote: > > Thank you, Roberto, > > > > I will investigate closer this function in chimera. > > > > Sincerely, > > Dmitry > > > > *From: *Roberto Marabini <ro...@cn...> > *Sent: *Tuesday, June 29, 2021 12:24 PM > *To: *Mailing list for Scipion users <sci...@li...> > *Subject: *Re: [scipion-users] micelle density subtraction > > > > Hi, > > > > 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) > > > > > > Roberto > > > > On Tue, Jun 29, 2021 at 11:57 AM Dmitry A. Semchonok <sem...@gm...> > wrote: > > > > Dear colleagues, > > > > We need to subtract the detergent micelle density from the result 3D map. > > The idea to run the 3D refinement after the subtraction and with that > improve the resolution. > > > > What are the ways to do that? > > (We currently have no model of my 3D map). > > > > Thank you in advance. > > > > Sincerely, > > Dmitry > > > > > > _______________________________________________ > 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 > |
