Re: [scipion-users] Export particles from cryosparc

[Grigory S. <sha...@gm...>]

Hi Dmitry,

I'll try to reproduce the error when I get a chance

On Wed, May 19, 2021, 09:41 Pablo Conesa <pc...@cn...> wrote:

> I see, maybe we can arrange a tele conf to see in detail what is wrong.
> I'll contact you.
> On 19/5/21 10:26, Dmitry Semchonok wrote:
>
> Dear Pablo and Grigory,
>
>
> Thank you!
>
> Yes, I am well aware of the fact that there is no info for the CTF etc :)
>
>
> All I need is just a nice aligned 2D set of images (from the set I
> imported)
>
> (Ideally I would like to have this set just from cryosparc but I have no
> idea how to do that right away :) )
>
> Please see the log of relion
>
>
>
> RUNNING PROTOCOL -----------------
> 00002:   Hostname: cryoem01
> 00003:   PID: 36440
> 00004:   pyworkflow: 3.0.13
> 00005:   plugin: relion
> 00006:   plugin v: 3.1.2
> 00007:   currentDir: /data1/ScipionUserData/projects/Caro__helix
> 00008:   workingDir: Runs/001735_ProtRelionClassify2D
> 00009:   runMode: Continue
> 00010:             MPI: 3
> 00011:         threads: 3
> 00012:    Starting at step: 1
> 00013:    Running steps
> 00014:   STARTED: convertInputStep, step 1, time 2021-05-18 15:06:21.557294
> 00015:   Converting set from
> 'Runs/001662_ProtImportParticles/particles.sqlite' into
> 'Runs/001735_ProtRelionClassify2D/input_particles.star'
> 00016:   convertBinaryFiles: creating soft links.
> 00017:      Root: Runs/001735_ProtRelionClassify2D/extra/input ->
> Runs/001662_ProtImportParticles/extra
> 00018:   FINISHED: convertInputStep, step 1, time 2021-05-18
> 15:06:22.474076
> 00019:   STARTED: runRelionStep, step 2, time 2021-05-18 15:06:22.502665
> 00020:    mpirun -np 3  `which relion_refine_mpi` --i
> Runs/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
> 690 --zero_mask  --K 64 --norm  --scale  --o
> Runs/001735_ProtRelionClassify2D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3
> 00021:   RELION version: 3.1.2
> 00022:   Precision: BASE=double, CUDA-ACC=single
> 00023:
> 00024:    === RELION MPI setup ===
> 00025:    + Number of MPI processes             = 3
> 00026:    + Number of threads per MPI process   = 3
> 00027:    + Total number of threads therefore   = 9
> 00028:    + Leader  (0) runs on host            = cryoem01
> 00029:    + Follower     1 runs on host            = cryoem01
> 00030:    + Follower     2 runs on host            = cryoem01
> 00031:    =================
> 00032:    uniqueHost cryoem01 has 2 ranks.
> 00033:   GPU-ids not specified for this rank, threads will automatically
> be mapped to available devices.
> 00034:    Thread 0 on follower 1 mapped to device 0
> 00035:    Thread 1 on follower 1 mapped to device 0
> 00036:    Thread 2 on follower 1 mapped to device 0
> 00037:   GPU-ids not specified for this rank, threads will automatically
> be mapped to available devices.
> 00038:    Thread 0 on follower 2 mapped to device 1
> 00039:    Thread 1 on follower 2 mapped to device 1
> 00040:    Thread 2 on follower 2 mapped to device 1
> 00041:    Running CPU instructions in double precision.
> 00042:    + WARNING: Changing psi sampling rate (before oversampling) to
> 5.625 degrees, for more efficient GPU calculations
> 00043:    + On host cryoem01: free scratch space = 447.485 Gb.
> 00044:    Copying particles to scratch directory:
> /data1/new_scratch/relion_volatile/
> 00045:   000/??? sec ~~(,_,">
>              [oo]
> 00046:      0/   0 sec ~~(,_,">in:
> /opt/Scipion3/software/em/relion-3.1.2/src/rwMRC.h, line 192
> 00047:   ERROR:
> 00048:   readMRC: Image number 11 exceeds stack size 1 of image
> 000011@Runs/001735_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
> 00049:   === Backtrace  ===
> 00050:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x4786a1]
> 00051:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0x99f)
> [0x4b210f]
> 00052:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x17b)
> [0x4b407b]
> 00053:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN10Experiment22copyParticlesToScratchEibbd+0xda7)
> [0x5b8f87]
> 00054:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x210)
> [0x498540]
> 00055:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9aa)
> [0x49ab2a]
> 00056:
> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(main+0x55)
> [0x4322a5]
> 00057:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fea6a54e555]
> 00058:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi()
> [0x435fbf]
> 00059:   ==================
> 00060:   ERROR:
> 00061:   readMRC: Image number 11 exceeds stack size 1 of image
> 000011@Runs/001735_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
> 00062:   application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> 00063:   Traceback (most recent call last):
> 00064:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
> 00065:       self._run()
> 00066:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
> 00067:       resultFiles = self._runFunc()
> 00068:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
> 00069:       return self._func(*self._args)
> 00070:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 811, in runRelionStep
> 00071:       self.runJob(self._getProgram(), params)
> 00072:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1388, in runJob
> 00073:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00074:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
> 00075:       process.runJob(log, programName, params,
> 00076:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
> 00077:       return runCommand(command, env, cwd)
> 00078:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
> 00079:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
> 00080:     File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364,
> in check_call
> 00081:       raise CalledProcessError(retcode, cmd)
> 00082:   subprocess.CalledProcessError: Command ' mpirun -np 3  `which
> relion_refine_mpi` --i
> Runs/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
> 690 --zero_mask  --K 64 --norm  --scale  --o
> Runs/001735_ProtRelionClassify2D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned
> non-zero exit status 1.
> 00083:   Protocol failed: Command ' mpirun -np 3  `which
> relion_refine_mpi` --i
> Runs/001735_ProtRelionClassify2D/input_particles.star --particle_diameter
> 690 --zero_mask  --K 64 --norm  --scale  --o
> Runs/001735_ProtRelionClassify2D/extra/relion --oversampling 1
> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned
> non-zero exit status 1.
> 00084:   FAILED: runRelionStep, step 2, time 2021-05-18 15:06:24.609548
> 00085:   *** Last status is failed
> 00086:   ------------------- PROTOCOL FAILED (DONE 2/3)
>
>
> *Additionally,*
>
> So it seemed from the first look that there is some issue with the image
> 11 — I delete the image 11 but the problem still remained.
>
>
>
>
> *Optionally,*
>
> I believe that xmipp-2D should work but I did not try it yet.
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
>
>
>
>
>
>
> On 19. May 2021, at 10:13, Pablo Conesa <pc...@cn...> wrote:
>
> Hi! So, I think Grigory is right, you've gone through  the import
> particles "without metadata info" therefore you only have the images
> without any alignment information.
>
>
> In theory, 2d classification should work with this kind of import. Could
> you please share the logs of one of the relion classification?
> On 19/5/21 9:26, Dmitry Semchonok wrote:
>
> Dear Grigory,
>
>
> I did nothing much, just tried to start relion 2D // or cryosparc.
>
>
> The only thing I tried additionally since I could no proceed is to a)
> change the box size; b) just resave the subset with the same number of
> images.
>
>
> Please see the image.
>
> <Screenshot 2021-05-19 at 09.23.41.png>
>
>
>  Thank you
>
> Sincerely,
>
> Dmitry
>
>
> On 18. May 2021, at 15:19, Grigory Sharov <sha...@gm...>
> wrote:
>
> Hi,
>
> I imagine you have 624 micrographs, so particles are exported to mrc on a
> mic basis. I see you used the "files" option to import mrcs particles into
> Scipion.  This means the imported particles have no metadata except pixel
> size you provided.
>
> What did you do with them after import?
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Tue, May 18, 2021 at 2:12 PM Dmitry Semchonok <Sem...@gm...>
> wrote:
>
>> Dear Grigory,
>>
>> Yes I did that — the particles are looking fine.
>>
>>
>> I guess the issue still comes from the fact that originally in cryosparc
>> Export the stacks of particle were placed into 624 mrc. But the number of
>> particles is about 44 818.  So even after the renaming and the export I see
>> this in SCIPION export log
>>
>> <Screenshot 2021-05-18 at 15.09.11.png>
>>
>> What I guess may help is if I somehow combine all those files in 1 mrcs
>> first and then add import them to SCIPION.
>> Do you perhaps know how to do that?
>>
>> Thank you
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>> On 18. May 2021, at 15:02, Grigory Sharov <sha...@gm...>
>> wrote:
>>
>> Hi Dmitry,
>>
>> as the error states your star file points to a non-existing image in the
>> mrcs stack.  You need to check first if you import from cryosparc with mrcs
>> worked correctly (open / display particles) then trace all the steps you
>> did before 2D classification.
>>
>> Best regards,
>> Grigory
>>
>>
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Tue, May 18, 2021 at 1:25 PM Dmitry Semchonok <Sem...@gm...>
>> wrote:
>>
>>> Dear Pablo,
>>>
>>>
>>> Thank you. I heard about this option. For that I guess the
>>> https://pypi.org/project/cs2star/ needs to be installed.
>>>
>>>
>>>
>>>
>>> In Cryosparc itself there is an option to export files. And then what we
>>> get is the mrc files with different number of particles in each.
>>>
>>> It appeared to be possible to rename mrc —> to —>mrcs. Then SCIPION can
>>> import those particles.
>>>
>>> Currently the problem is that not relion nor cryosparc can run these
>>> particles.
>>>
>>>
>>>
>>>
>>> Relion stops with error:
>>>
>>>
>>> 00001:   RUNNING PROTOCOL -----------------
>>> 00002:   Hostname: cryoem01
>>> 00003:   PID: 46455
>>> 00004:   pyworkflow: 3.0.13
>>> 00005:   plugin: relion
>>> 00006:   plugin v: 3.1.2
>>> 00007:   currentDir: /data1/ScipionUserData/projects/Caro__helix
>>> 00008:   workingDir: Runs/001546_ProtRelionClassify2D
>>> 00009:   runMode: Continue
>>> 00010:             MPI: 3
>>> 00011:         threads: 3
>>> 00012:    Starting at step: 1
>>> 00013:    Running steps
>>> 00014:   STARTED: convertInputStep, step 1, time 2021-05-18
>>> 12:33:26.198123
>>> 00015:   Converting set from
>>> 'Runs/001492_ProtUserSubSet/particles.sqlite' into
>>> 'Runs/001546_ProtRelionClassify2D/input_particles.star'
>>> 00016:   convertBinaryFiles: creating soft links.
>>> 00017:      Root: Runs/001546_ProtRelionClassify2D/extra/input ->
>>> Runs/001057_ProtImportParticles/extra
>>> 00018:   FINISHED: convertInputStep, step 1, time 2021-05-18
>>> 12:33:27.117588
>>> 00019:   STARTED: runRelionStep, step 2, time 2021-05-18 12:33:27.145974
>>> 00020:    mpirun -np 3  `which relion_refine_mpi` --i
>>> Runs/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>> Runs/001546_ProtRelionClassify2D/extra/relion --oversampling 1
>>> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
>>> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>>>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3
>>> 00021:   RELION version: 3.1.2
>>> 00022:   Precision: BASE=double, CUDA-ACC=single
>>> 00023:
>>> 00024:    === RELION MPI setup ===
>>> 00025:    + Number of MPI processes             = 3
>>> 00026:    + Number of threads per MPI process   = 3
>>> 00027:    + Total number of threads therefore   = 9
>>> 00028:    + Leader  (0) runs on host            = cryoem01
>>> 00029:    + Follower     1 runs on host            = cryoem01
>>> 00030:    + Follower     2 runs on host            = cryoem01
>>> 00031:    =================
>>> 00032:    uniqueHost cryoem01 has 2 ranks.
>>> 00033:   GPU-ids not specified for this rank, threads will automatically
>>> be mapped to available devices.
>>> 00034:    Thread 0 on follower 1 mapped to device 0
>>> 00035:    Thread 1 on follower 1 mapped to device 0
>>> 00036:    Thread 2 on follower 1 mapped to device 0
>>> 00037:   GPU-ids not specified for this rank, threads will automatically
>>> be mapped to available devices.
>>> 00038:    Thread 0 on follower 2 mapped to device 1
>>> 00039:    Thread 1 on follower 2 mapped to device 1
>>> 00040:    Thread 2 on follower 2 mapped to device 1
>>> 00041:    Running CPU instructions in double precision.
>>> 00042:    + WARNING: Changing psi sampling rate (before oversampling) to
>>> 5.625 degrees, for more efficient GPU calculations
>>> 00043:    + On host cryoem01: free scratch space = 448.252 Gb.
>>> 00044:    Copying particles to scratch directory:
>>> /data1/new_scratch/relion_volatile/
>>> 00045:   000/??? sec ~~(,_,">
>>>                [oo]
>>> 00046:      1/  60 sec ~~(,_,">in:
>>> /opt/Scipion3/software/em/relion-3.1.2/src/rwMRC.h, line 192
>>> 00047:   ERROR:
>>> 00048:   readMRC: Image number 11 exceeds stack size 1 of image
>>> 000011@Runs/001546_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
>>> 00049:   === Backtrace  ===
>>> 00050:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
>>> [0x4786a1]
>>> 00051:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0x99f)
>>> [0x4b210f]
>>> 00052:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x17b)
>>> [0x4b407b]
>>> 00053:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN10Experiment22copyParticlesToScratchEibbd+0xda7)
>>> [0x5b8f87]
>>> 00054:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x210)
>>> [0x498540]
>>> 00055:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x9aa)
>>> [0x49ab2a]
>>> 00056:
>>> /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi(main+0x55)
>>> [0x4322a5]
>>> 00057:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f657f51a555]
>>> 00058:   /opt/Scipion3/software/em/relion-3.1.2/bin/relion_refine_mpi()
>>> [0x435fbf]
>>> 00059:   ==================
>>> 00060:   ERROR:
>>> 00061:   readMRC: Image number 11 exceeds stack size 1 of image
>>> 000011@Runs/001546_ProtRelionClassify2D/extra/input/1024562735536827037_FoilHole_1618719_Data_1621438_1621440_20200703_085118_Fractions_patch_aligned_doseweighted_particles.mrcs
>>> 00062:   application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
>>> 00063:   Traceback (most recent call last):
>>> 00064:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 197, in run
>>> 00065:       self._run()
>>> 00066:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 248, in _run
>>> 00067:       resultFiles = self._runFunc()
>>> 00068:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 244, in _runFunc
>>> 00069:       return self._func(*self._args)
>>> 00070:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
>>> line 811, in runRelionStep
>>> 00071:       self.runJob(self._getProgram(), params)
>>> 00072:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
>>> line 1388, in runJob
>>> 00073:       self._stepsExecutor.runJob(self._log, program, arguments,
>>> **kwargs)
>>> 00074:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
>>> line 65, in runJob
>>> 00075:       process.runJob(log, programName, params,
>>> 00076:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
>>> line 52, in runJob
>>> 00077:       return runCommand(command, env, cwd)
>>> 00078:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
>>> line 67, in runCommand
>>> 00079:       check_call(command, shell=True, stdout=sys.stdout,
>>> stderr=sys.stderr,
>>> 00080:     File
>>> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364,
>>> in check_call
>>> 00081:       raise CalledProcessError(retcode, cmd)
>>> 00082:   subprocess.CalledProcessError: Command ' mpirun -np 3  `which
>>> relion_refine_mpi` --i
>>> Runs/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>> Runs/001546_ProtRelionClassify2D/extra/relion --oversampling 1
>>> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
>>> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>>>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned
>>> non-zero exit status 1.
>>> 00083:   Protocol failed: Command ' mpirun -np 3  `which
>>> relion_refine_mpi` --i
>>> Runs/001546_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 690 --zero_mask  --K 64 --norm  --scale  --o
>>> Runs/001546_ProtRelionClassify2D/extra/relion --oversampling 1
>>> --flatten_solvent  --tau2_fudge 2.0 --iter 25 --offset_range 5.0
>>> --offset_step 2.0 --psi_step 10.0 --dont_combine_weights_via_disc
>>>  --scratch_dir /data1/new_scratch/ --pool 3 --gpu   --j 3' returned
>>> non-zero exit status 1.
>>> 00084:   FAILED: runRelionStep, step 2, time 2021-05-18 12:33:29.230213
>>> 00085:   *** Last status is failed
>>> 00086:   ------------------- PROTOCOL FAILED (DONE 2/3)
>>>
>>>
>>> Cryosparc (in SCIPION) requires CTF to run.
>>>
>>>
>>>
>>> Thais is where I am now.
>>>
>>> Perhaps there is a solution?
>>>
>>>
>>> Sincerely,
>>> Dmitry
>>>
>>>
>>>
>>> On 18. May 2021, at 14:16, Pablo Conesa <pc...@cn...> wrote:
>>>
>>> Dear Dmitry, the import of CS metadata files (*.cs) is not supported in
>>> Scipion. Does CS has an option to export to star files. It rings a bell.
>>> On 18/5/21 9:53, Dmitry Semchonok wrote:
>>>
>>> Dear Grigory,
>>>
>>>
>>> The files are in mrc format.
>>>
>>>
>>> Please, let me try to explain more plan:
>>>
>>>  I have a project in cryosparc. There I have cryosparc selected 2D
>>> classes. I want to export the particles of those classes into SCIPION.
>>>
>>>  So I I pressed Export (fig 1) and the program(cryosparc) created the
>>> folder with mrc  + other files (fig 2;3). I looked into J48 and found many
>>> *.mrc files of the particles. But it is not 1 mrc = 1 particle. It seems to
>>> be a mrc stuck - so I have several files inside 1 *.mrc  (fig 4) (you can
>>> also notice that they all have different sizes)
>>>
>>>  So I need to export them somehow in SCIPION
>>>
>>>  For that, I used the SCIPION export - images protocol where for the
>>> files to add I put *.mrc. But the protocol seems to be added only 1 mrc as
>>> 1 picture and instead of having 46392 particles I have ~600 particles.
>>>
>>>  (Also the geometry seems not preserved).
>>>
>>>
>>> So my question how to export the particles from cryosparc into SCIPION
>>> correctly?
>>>
>>>
>>>  Thank you!
>>>
>>>
>>>
>>>  https://disk.yandex.com/d/Fv3Q1lpwEzSisg
>>>
>>>  Sincerely,
>>>
>>> Dmitry
>>>
>>>
>>>
>>> On 17. May 2021, at 18:12, Grigory Sharov <sha...@gm...>
>>> wrote:
>>>
>>> Hi Dmitry,
>>>
>>> mrc stacks should have "mrcs" extension. Is this the problem you are
>>> getting?
>>>
>>> Best regards,
>>> Grigory
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> Grigory Sharov, Ph.D.
>>>
>>> MRC Laboratory of Molecular Biology,
>>> Francis Crick Avenue,
>>> Cambridge Biomedical Campus,
>>> Cambridge CB2 0QH, UK.
>>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>>> e-mail: gs...@mr...
>>>
>>>
>>> On Mon, May 17, 2021 at 4:49 PM Dmitry Semchonok <Sem...@gm...>
>>> wrote:
>>>
>>>> Dear colleagues,
>>>>
>>>>  I would like to export the particles from cryosparc to SCIPION.
>>>>
>>>>  How to do that?
>>>>
>>>>
>>>>
>>>>
>>>> What I tried:
>>>>
>>>>
>>>> 1.     In cryosparc I pressed Export – to export the particles I am
>>>> interested in.
>>>>
>>>> 2.     In the folder Export – I found many mrc stacks with particles
>>>> in each.
>>>>
>>>> 3.     I tried to export them to SCIPION using Export particles but
>>>> instead of reading each stack and combine them in the 1 dataset I received
>>>> 1 particle / per each mrc stack.
>>>>
>>>>
>>>> Any ideas?
>>>>
>>>>
>>>> Thank you
>>>>
>>>>  Sincerely,
>>>>
>>>> Dmitry
>>>>
>>>> _______________________________________________
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>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
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>>>
>>>
>>>
>>> _______________________________________________
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>>>
>>> --
>>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es/> team*
>>> _______________________________________________
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>>>
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