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Re: [scipion-users] micelle density subtraction
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From: Marta M. <mm...@cn...> - 2021-06-30 10:51:55
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Hi Dmitry,
to discard other problems, can you check that both maps are perfectly
aligned in Scipion?
Cheers,
MARTA
Quoting "Dmitry A. Semchonok" <sem...@gm...>:
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> 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[1] for Windows 10
>
>
>
> FROM: Roberto Marabini[2]
> SENT: Wednesday, June 30, 2021 12:35 AM
> TO: Mailing list for Scipion users[3]
> 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[2]
>> SENT: Tuesday, June 29, 2021 12:24 PM
>> TO: Mailing list for Scipion users[3]
>> 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
>>
>>
>
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>
>
>
>
>
> Links:
> ------
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> [2] mailto:ro...@cn...
> [3] mailto:sci...@li...
--
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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