scipion-users — Mailing list for Scipion users

[scipion-users] relion_localized_reconstruction - weird results

[Stefano T. <tr...@cb...>]

 

Dear all 

(sorry if I am sending this message to two mailing lists at the same
time) 

I am finding some weird results (see the attached picture) after using
the _relion_localized_reconstruction.py_ procedure described by Ilca et
al (2015) and implemented in Scipion. 

The picture on the left shows the C1 reconstruction of an icosahedral
virus starting from a set of previously aligned, symmetry-expanded and
signal-subtracted particles (using RELION 3.0). The reconstructed
density corresponds to a protein pentamer centred on one of the 5-fold
symmetry axes (plus some residual signal around the rest of the viral
particle). The reconstruction box size is 356x356x356 pixels. 

The picture on the right shows the reconstruction obtained after
sub-particle extraction into a smaller box (96x96x96). Sub-particle
extraction was carried out without realignment in C1 and without signal
subtraction (for the starting particles had already been
symmetry-expanded and signal-subtracted; the details of the command
parameters used are shown in the picture). 

Surprisingly, the reconstruction from the extracted sub-particles looks
significantly different (worse) than the original one (I would expect
them to be the same within the 96x96x96 box). 

Any reason that could explain that? Did I use some wrong parameter ? Is
this a bug ? 

Rem: the alignment angles in the original and sub-particle star files
seem to be correct (do not know if the same goes for the sub-particle
origins). 

Best regards 

-- 
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-------------------------------------
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-------------------------------------
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-------------------------------------

 
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Re: [scipion-users] Use of masks in MonoRes and LocalDebur

[JOSE L. V. P. <jl...@cn...>]

Dear Matthieu,

Thanks for reporting the issue.

> Is it possible to use a non-spherical mask to restrict where MonoRes and
> LocalDeblur analysis run in a map? I've not seen this option in these
> programs but I'm asking anyhow in case there are some suggestions about how
> to achieve this.

Regarding with MonoRes. The main aspect is that it requires noise to  
determine the resolution. A tight mask to the map allows to  
distinguish the noisy region from the protein, and it defines the  
region for resolution analysis. The spherical mask you comment is  
other issue, it defines the region where noise and protein are. Note,  
that some maps presents noise-free regions outside of a spherical  
region (for instance because particles where masked with a circle or  
the reconstruction used a sphere). The tight mask that MonoRes  
requires only defines the protein.

The spherical mask should not affect to the computational times. I  
think it is due to the your map is large, I guess that probably it  
will be larger than 1000X1000x1000, am I right?. Hence I estimate that  
monores can take 2-4h?. Here is the problem, because internally  
LocalDeBlur runs MonoRes several times and as a consequence it will  
take more time (more than a day, could it be?)

We have a solution for decreasing (a litle bit) MonoRes time and  
therefore LocalDeblur, unfortunately, we are developing it.

> If I could run these programs on a 15% segment of these helical maps (which
> contains all the information), then I could just apply helical symmetry to
> get the full map and the processing would be much faster.
> I suspect that pre-masking the half-maps or giving a mask to MonoRes that
> does not include all the signal of the macromolecule in the map would
> negatively impact the noise estimation in MonoRes.

If I understood right, what you are saying is that due to your map  
presents symmetry, you want to apply MonoRes/LocalDeBlur to the unit  
cell, and then make use of the symmetry to reover the map.
Honestly, I never did it, but you can do to get MonoRes result but is  
not applicable to LocaldeBlur because the current implementation only  
uses a single map. The use of half maps in LocalDeBlur is in our  
development list.
If you want to do it with MonoRes. You  need to create a mask that  
defines the region of your unit cell, and then you provide to monores  
the half maps and that mask. The noise using half maps should only be  
calculated by halves difference.

By the way, what Scipion version are you using? This is important to  
know how fast your MonoRes version is.

I expect to be useful

Thanks again for your questions and comments

Kind regards

Jose Luis Vilas

Matthieu Benoit <bio...@gm...> escribió:

> Hi,
>
> Is it possible to use a non-spherical mask to restrict where MonoRes and
> LocalDeblur analysis run in a map? I've not seen this option in these
> programs but I'm asking anyhow in case there are some suggestions about how
> to achieve this. I'm asking because I have over 20 large maps with helical
> symmetry that I'd like to postprocess. I like the MonoRes/LocalDeblur
> results but the computation takes 2 days for each map on my workstation.

> If I could run these programs on a 15% segment of these helical maps (which
> contains all the information), then I could just apply helical symmetry to
> get the full map and the processing would be much faster.
> I suspect that pre-masking the half-maps or giving a mask to MonoRes that
> does not include all the signal of the macromolecule in the map would
> negatively impact the noise estimation in MonoRes.
>
> Thanks for any advice,
>
> Best,
>
> Matthieu

[scipion-users] Use of masks in MonoRes and LocalDebur

[Matthieu B. <bio...@gm...>]

Hi,

Is it possible to use a non-spherical mask to restrict where MonoRes and
LocalDeblur analysis run in a map? I've not seen this option in these
programs but I'm asking anyhow in case there are some suggestions about how
to achieve this. I'm asking because I have over 20 large maps with helical
symmetry that I'd like to postprocess. I like the MonoRes/LocalDeblur
results but the computation takes 2 days for each map on my workstation. If
I could run these programs on a 15% segment of these helical maps (which
contains all the information), then I could just apply helical symmetry to
get the full map and the processing would be much faster.
I suspect that pre-masking the half-maps or giving a mask to MonoRes that
does not include all the signal of the macromolecule in the map would
negatively impact the noise estimation in MonoRes.

Thanks for any advice,

Best,

Matthieu

Re: [scipion-users] question about scipion.config

[Yashar S. <sa...@em...>]

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Re: [scipion-users] Can't import star file into scipion

[Dr M. Y. <men...@ma...>]

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Re: [scipion-users] xmipp movie extract 'ProgrammingError' recursive use of commas not allowed

[Jose M. de la R. T. <del...@gm...>]

Dear Teige,

>From your error log it seems that there is a bug in this Xmipp protocol in
line:

00095:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/
packages/xmipp3/protocol_extract_particles_movies.py", line 434, in
_filterMovie
00096:       micrograph = micSet[movieId]

Where the micSet (internally a .sqlite database) is accessed from multiple
threads. I think this should be fixed by removing this query in the way it
is now.
In the meantime, as David suggested, you could try to run with only 1
processor, but not sure how long it will take.

I'm sorry for this issue.
Best,
Jose Miguel


On Tue, Aug 7, 2018 at 4:03 PM David Maluenda <dma...@cn...> wrote:

> This sounds like it's trying to read/write to .sqlite in threads and
> sqlite doesn't support threating.
>
> Therefore, try to run the protocol with *1 thread* and *1 MPI*.
>
>
> Thanks for your comment!
>
> <http://ucm.es/>
>
> *_____Dr. David Maluenda Niubó*
> dma...@cn... - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
> BioComputing Unit <http://biocomputingunit.es/>
>
> This email message and any documents attached to it may contain
> confidential or legally protected material and are intended solely for the
> use of the individual or organization to whom they are addressed. We remind
> you that if you are not the intended recipient of this email message or the
> person responsible for processing it, then you are not authorized to read,
> save, modify, send, copy or disclose any of its contents. If you have
> received this email message by mistake, we kindly ask you to inform the
> sender of this and to eliminate both the message and any attachments it
> carries from your account. Thank you for your collaboration.
>
>
>
> On Tue, Aug 7, 2018 at 2:49 PM Matthews-Palmer, Teige Rowan Seal <
> t.m...@im...> wrote:
>
>> Dear Scipion users,
>>
>> I am getting the following error in Caligula v1.2, from the protocol
>> xmipp3 extract movie particles:
>>
>> Any ideas or help greatly appreciated.
>> All the best,
>>
>> Teige
>>
>>
>> 00086:   Traceback (most recent call last):
>> 00087:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/executor.py",
>> line 137, in run
>> 00088:       self.step._run()  # not self.step.run() , to avoid race
>> conditions
>> 00089:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
>> line 233, in _run
>> 00090:       resultFiles = self._runFunc()
>> 00091:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
>> line 229, in _runFunc
>> 00092:       return self._func(*self._args)
>> 00093:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/protocol/protocol_movies.py",
>> line 234, in processMovieStep
>> 00094:       if self._filterMovie(movie):
>> 00095:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py",
>> line 434, in _filterMovie
>> 00096:       micrograph = micSet[movieId]
>> 00097:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1040,
>> in __getitem__
>> 00098:       return self._getMapper().selectById(itemId)
>> 00099:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1025,
>> in _getMapper
>> 00100:       self.load()
>> 00101:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1117,
>> in load
>> 00102:       self._idCount = self._mapper.maxId()
>> 00103:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
>> 900, in maxId
>> 00104:       return 0 if self.doCreateTables else self.db.maxId()
>>
>>
>> *00105:     File
>> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
>> 1201, in maxId 00106:
>> self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)')) 00107:
>> ProgrammingError: Recursive use of cursors not allowed.*
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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> _______________________________________________
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Re: [scipion-users] xmipp movie extract 'ProgrammingError' recursive use of commas not allowed

[David M. <dma...@cn...>]

This sounds like it's trying to read/write to .sqlite in threads and sqlite
doesn't support threating.

Therefore, try to run the protocol with *1 thread* and *1 MPI*.


Thanks for your comment!

<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

This email message and any documents attached to it may contain
confidential or legally protected material and are intended solely for the
use of the individual or organization to whom they are addressed. We remind
you that if you are not the intended recipient of this email message or the
person responsible for processing it, then you are not authorized to read,
save, modify, send, copy or disclose any of its contents. If you have
received this email message by mistake, we kindly ask you to inform the
sender of this and to eliminate both the message and any attachments it
carries from your account. Thank you for your collaboration.



On Tue, Aug 7, 2018 at 2:49 PM Matthews-Palmer, Teige Rowan Seal <
t.m...@im...> wrote:

> Dear Scipion users,
>
> I am getting the following error in Caligula v1.2, from the protocol
> xmipp3 extract movie particles:
>
> Any ideas or help greatly appreciated.
> All the best,
>
> Teige
>
>
> 00086:   Traceback (most recent call last):
> 00087:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/executor.py",
> line 137, in run
> 00088:       self.step._run()  # not self.step.run() , to avoid race
> conditions
> 00089:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
> line 233, in _run
> 00090:       resultFiles = self._runFunc()
> 00091:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py",
> line 229, in _runFunc
> 00092:       return self._func(*self._args)
> 00093:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/protocol/protocol_movies.py",
> line 234, in processMovieStep
> 00094:       if self._filterMovie(movie):
> 00095:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py",
> line 434, in _filterMovie
> 00096:       micrograph = micSet[movieId]
> 00097:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1040,
> in __getitem__
> 00098:       return self._getMapper().selectById(itemId)
> 00099:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1025,
> in _getMapper
> 00100:       self.load()
> 00101:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1117,
> in load
> 00102:       self._idCount = self._mapper.maxId()
> 00103:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
> 900, in maxId
> 00104:       return 0 if self.doCreateTables else self.db.maxId()
>
>
> *00105:     File
> "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line
> 1201, in maxId 00106:
> self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)')) 00107:
> ProgrammingError: Recursive use of cursors not allowed.*
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] xmipp movie extract 'ProgrammingError' recursive use of commas not allowed

[Matthews-Palmer, T. R. S. <t.m...@im...>]

Dear Scipion users,

I am getting the following error in Caligula v1.2, from the protocol xmipp3 extract movie particles:

Any ideas or help greatly appreciated.
All the best,

Teige

00086:   Traceback (most recent call last):
00087:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/executor.py", line 137, in run
00088:       self.step._run()  # not self.step.run() , to avoid race conditions
00089:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py", line 233, in _run
00090:       resultFiles = self._runFunc()
00091:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/protocol/protocol.py", line 229, in _runFunc
00092:       return self._func(*self._args)
00093:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/protocol/protocol_movies.py", line 234, in processMovieStep
00094:       if self._filterMovie(movie):
00095:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py", line 434, in _filterMovie
00096:       micrograph = micSet[movieId]
00097:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1040, in __getitem__
00098:       return self._getMapper().selectById(itemId)
00099:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1025, in _getMapper
00100:       self.load()
00101:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/object.py", line 1117, in load
00102:       self._idCount = self._mapper.maxId()
00103:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line 900, in maxId
00104:       return 0 if self.doCreateTables else self.db.maxId()
00105:     File "/beebylab/software/scipion/1.2/scipion/pyworkflow/mapper/sqlite.py", line 1201, in maxId
00106:       self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)'))
00107:   ProgrammingError: Recursive use of cursors not allowed.

Re: [scipion-users] importing micrographs.star

[Jose M. de la R. T. <del...@gm...>]

Yes, but we need to double check. We had an issue here importing
coordinates from Warp.
It seems that for some particles it wrote the FOM value in the star files
and for others not. This caused a
fail in the import protocol. We did a quick and dirty workaround, but not a
general solution.

On Tue, Aug 7, 2018 at 9:15 AM Juha Huiskonen <ju...@st...> wrote:

> Hi Jose Miguel,
>
> Importing particles should work already, as Warp writes a Relion style
> STAR file for particles with CTF info.  Just the option for importing
> micrographs using a STAR file is missing.
>
> Best wishes,
> Juha
>
> On Tue, Aug 7, 2018 at 10:12 AM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Yes, that is a good idea to add the import of particles (and maybe
>> micrographs/ctf) from Warp.
>>
>> Best,
>> Jose Miguel
>>
>> On Tue, Aug 7, 2018 at 9:08 AM Juha Huiskonen <ju...@st...>
>> wrote:
>>
>>> Hi Pablo,
>>>
>>> It looks like a normal Relion micrographs star file.  Here's an idea: I
>>> could run particle extraction, then stop it, replace input_particles.star
>>> with my file, and then continue the run.  Do you think this would work? (
>>> It's not so simple to to turn it into CTF files. )
>>>
>>> Can you please add this import option in the wish list, thanks.
>>>
>>> Best wishes,
>>> Juha
>>>
>>>
>>> On Tue, Aug 7, 2018 at 10:02 AM Pablo Conesa <pc...@cn...>
>>> wrote:
>>>
>>>> How does the star file look like?
>>>>
>>>> it might be possible to turn it into a ctf import file?
>>>>
>>>> I know this is a hack but can't see something better..
>>>>
>>>> Juha, do you mind to send us the star file to have a look at it.
>>>>
>>>> On 05/08/18 15:26, Juha Huiskonen wrote:
>>>>
>>>> Hi All,
>>>>
>>>> I have a STAR file with micrograph metadata, including CTF parameters
>>>> (produced in Warp).   It seems that currently a STAR file input is
>>>> available only for particles and not for micrographs.  Is there any
>>>> workaround to import the micrographs at the moment, with their CTF info?
>>>>
>>>> Best wishes,
>>>> Juha
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
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>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>

Re: [scipion-users] importing micrographs.star

[Juha H. <ju...@st...>]

Hi Jose Miguel,

Importing particles should work already, as Warp writes a Relion style STAR
file for particles with CTF info.  Just the option for importing
micrographs using a STAR file is missing.

Best wishes,
Juha

On Tue, Aug 7, 2018 at 10:12 AM Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Yes, that is a good idea to add the import of particles (and maybe
> micrographs/ctf) from Warp.
>
> Best,
> Jose Miguel
>
> On Tue, Aug 7, 2018 at 9:08 AM Juha Huiskonen <ju...@st...>
> wrote:
>
>> Hi Pablo,
>>
>> It looks like a normal Relion micrographs star file.  Here's an idea: I
>> could run particle extraction, then stop it, replace input_particles.star
>> with my file, and then continue the run.  Do you think this would work? (
>> It's not so simple to to turn it into CTF files. )
>>
>> Can you please add this import option in the wish list, thanks.
>>
>> Best wishes,
>> Juha
>>
>>
>> On Tue, Aug 7, 2018 at 10:02 AM Pablo Conesa <pc...@cn...> wrote:
>>
>>> How does the star file look like?
>>>
>>> it might be possible to turn it into a ctf import file?
>>>
>>> I know this is a hack but can't see something better..
>>>
>>> Juha, do you mind to send us the star file to have a look at it.
>>>
>>> On 05/08/18 15:26, Juha Huiskonen wrote:
>>>
>>> Hi All,
>>>
>>> I have a STAR file with micrograph metadata, including CTF parameters
>>> (produced in Warp).   It seems that currently a STAR file input is
>>> available only for particles and not for micrographs.  Is there any
>>> workaround to import the micrographs at the moment, with their CTF info?
>>>
>>> Best wishes,
>>> Juha
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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>

Re: [scipion-users] importing micrographs.star

[Pablo C. <pc...@cn...>]

Added: https://github.com/I2PC/scipion/issues/1719


On 07/08/18 09:07, Juha Huiskonen wrote:
> Hi Pablo,
>
> It looks like a normal Relion micrographs star file. Here's an idea: I 
> could run particle extraction, then stop it, replace 
> input_particles.star with my file, and then continue the run.  Do you 
> think this would work? ( It's not so simple to to turn it into CTF 
> files. )
>
> Can you please add this import option in the wish list, thanks.
>
> Best wishes,
> Juha
>
>
> On Tue, Aug 7, 2018 at 10:02 AM Pablo Conesa <pc...@cn... 
> <mailto:pc...@cn...>> wrote:
>
>     How does the star file look like?
>
>     it might be possible to turn it into a ctf import file?
>
>     I know this is a hack but can't see something better..
>
>     Juha, do you mind to send us the star file to have a look at it.
>
>
>     On 05/08/18 15:26, Juha Huiskonen wrote:
>>     Hi All,
>>
>>     I have a STAR file with micrograph metadata, including CTF
>>     parameters (produced in Warp).   It seems that currently a STAR
>>     file input is available only for particles and not for
>>     micrographs.  Is there any workaround to import the micrographs
>>     at the moment, with their CTF info?
>>
>>     Best wishes,
>>     Juha
>>
>>
>>     ------------------------------------------------------------------------------
>>     Check out the vibrant tech community on one of the world's most
>>     engaging tech sites, Slashdot.org!http://sdm.link/slashdot
>>
>>
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>     ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, Slashdot.org!
>     http://sdm.link/slashdot_______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
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Re: [scipion-users] importing micrographs.star

[Jose M. de la R. T. <del...@gm...>]

Yes, that is a good idea to add the import of particles (and maybe
micrographs/ctf) from Warp.

Best,
Jose Miguel

On Tue, Aug 7, 2018 at 9:08 AM Juha Huiskonen <ju...@st...> wrote:

> Hi Pablo,
>
> It looks like a normal Relion micrographs star file.  Here's an idea: I
> could run particle extraction, then stop it, replace input_particles.star
> with my file, and then continue the run.  Do you think this would work? (
> It's not so simple to to turn it into CTF files. )
>
> Can you please add this import option in the wish list, thanks.
>
> Best wishes,
> Juha
>
>
> On Tue, Aug 7, 2018 at 10:02 AM Pablo Conesa <pc...@cn...> wrote:
>
>> How does the star file look like?
>>
>> it might be possible to turn it into a ctf import file?
>>
>> I know this is a hack but can't see something better..
>>
>> Juha, do you mind to send us the star file to have a look at it.
>>
>> On 05/08/18 15:26, Juha Huiskonen wrote:
>>
>> Hi All,
>>
>> I have a STAR file with micrograph metadata, including CTF parameters
>> (produced in Warp).   It seems that currently a STAR file input is
>> available only for particles and not for micrographs.  Is there any
>> workaround to import the micrographs at the moment, with their CTF info?
>>
>> Best wishes,
>> Juha
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] importing micrographs.star

[Juha H. <ju...@st...>]

Hi Pablo,

It looks like a normal Relion micrographs star file.  Here's an idea: I
could run particle extraction, then stop it, replace input_particles.star
with my file, and then continue the run.  Do you think this would work? (
It's not so simple to to turn it into CTF files. )

Can you please add this import option in the wish list, thanks.

Best wishes,
Juha


On Tue, Aug 7, 2018 at 10:02 AM Pablo Conesa <pc...@cn...> wrote:

> How does the star file look like?
>
> it might be possible to turn it into a ctf import file?
>
> I know this is a hack but can't see something better..
>
> Juha, do you mind to send us the star file to have a look at it.
>
> On 05/08/18 15:26, Juha Huiskonen wrote:
>
> Hi All,
>
> I have a STAR file with micrograph metadata, including CTF parameters
> (produced in Warp).   It seems that currently a STAR file input is
> available only for particles and not for micrographs.  Is there any
> workaround to import the micrographs at the moment, with their CTF info?
>
> Best wishes,
> Juha
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] importing micrographs.star

[Pablo C. <pc...@cn...>]

How does the star file look like?

it might be possible to turn it into a ctf import file?

I know this is a hack but can't see something better..

Juha, do you mind to send us the star file to have a look at it.


On 05/08/18 15:26, Juha Huiskonen wrote:
> Hi All,
>
> I have a STAR file with micrograph metadata, including CTF parameters 
> (produced in Warp).   It seems that currently a STAR file input is 
> available only for particles and not for micrographs.  Is there any 
> workaround to import the micrographs at the moment, with their CTF info?
>
> Best wishes,
> Juha
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[scipion-users] importing micrographs.star

[Juha H. <ju...@st...>]

Hi All,

I have a STAR file with micrograph metadata, including CTF parameters
(produced in Warp).   It seems that currently a STAR file input is
available only for particles and not for micrographs.  Is there any
workaround to import the micrographs at the moment, with their CTF info?

Best wishes,
Juha

Re: [scipion-users] MonoRes issues

[JOSE L. V. P. <jl...@cn...>]

Dear Chen Sun,

First, thanks for using MonoRes.

Regarding with the error, I would say one of next reasons for this error.

1) MonoRes establish a comparison between signal and noise at  
different frequencies. The mask is used to localize the signal and the  
noise. A possible fail reason is if your volume (or halves) does not  
present noise, in that case, there is nothing to be compared and  
MonoRes cast and error.

2) An alternative is to check your mask, It should be binary, (in next  
release -soon- this condition it is not necessary).

4) If your virus was masked with an spherical mask, please provide the  
radius of that mask. You have to put enable the option mask radius.

I expect that one of this reason will solve your problem, otherwise,  
please write us again, and we go in more detail


Regards

Jose Luis Vilas

Quoting Chen Sun <su...@pu...>:

> Dear all,
>
>
> I am trying to use MonoRes to estimate the local resolution of my  
> virus map (320x320pixel box size). However, it failed more than four  
> times with the same error message which is copied below. Is it a  
> memory issue? I have run it successfully with a smaller map (256x256  
> pixel box size). Do anyone know how to work around this problem?
>
>
> The error message:
>
> Search of resolutions stopped due to mask has been completed
> 00114:   Segmentation fault (core dumped)
> 00115:   Traceback (most recent call last):
> 00116:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 186, in run
> 00117:       self._run()
> 00118:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 233, in _run
> 00119:       resultFiles = self._runFunc()
> 00120:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 229, in _runFunc
> 00121:       return self._func(*self._args)
> 00122:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/em/packages/xmipp3/protocol_resolution_monogenic_signal.py", line 252, in  
> resolutionMonogenicSignalStep
> 00123:       self.runJob('xmipp_resolution_monogenic_signal', params)
> 00124:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line  
> 1138, in runJob
> 00125:       self._stepsExecutor.runJob(self._log, program,  
> arguments, **kwargs)
> 00126:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/protocol/executor.py", line  
> 56, in runJob
> 00127:       env=env, cwd=cwd)
> 00128:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 51,  
> in runJob
> 00129:       return runCommand(command, env, cwd)
> 00130:     File  
> "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 65,  
> in runCommand
> 00131:       check_call(command, shell=True, stdout=sys.stdout,  
> stderr=sys.stderr, env=env, cwd=cwd)
> 00132:     File  
> "/net/apps/linux/scipion/1.2/software/lib/python2.7/subprocess.py",  
> line 186, in check_call
> 00133:       raise CalledProcessError(retcode, cmd)
> 00134:   CalledProcessError: Command  
> 'xmipp_resolution_monogenic_signal  --vol  
> Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2  
> Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol  
> Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask  
> Runs/000501_ProtImportMask/extra/mask.mrc --mask_out  
> Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o  
> Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate  
> 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes  
> 5.000000 --volumeRadius 160.000000 --chimera_volume  
> Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i  
> --significance 0.950000 --md_outputdata  
> Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume '  
> returned non-zero exit status 139
> 00135:   Protocol failed: Command 'xmipp_resolution_monogenic_signal  
>  --vol Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2  
> Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol  
> Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask  
> Runs/000501_ProtImportMask/extra/mask.mrc --mask_out  
> Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o  
> Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate  
> 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes  
> 5.000000 --volumeRadius 160.000000 --chimera_volume  
> Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i  
> --significance 0.950000 --md_outputdata  
> Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume '  
> returned non-zero exit status 139
> 00136:   FAILED: resolutionMonogenicSignalStep, step 2
>
>
> Thanks,
>
> Chen

[scipion-users] MonoRes issues

[Chen S. <su...@pu...>]

Dear all,


I am trying to use MonoRes to estimate the local resolution of my virus map (320x320pixel box size). However, it failed more than four times with the same error message which is copied below. Is it a memory issue? I have run it successfully with a smaller map (256x256 pixel box size). Do anyone know how to work around this problem?


The error message:

Search of resolutions stopped due to mask has been completed
00114:   Segmentation fault (core dumped)
00115:   Traceback (most recent call last):
00116:     File "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line 186, in run
00117:       self._run()
00118:     File "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line 233, in _run
00119:       resultFiles = self._runFunc()
00120:     File "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line 229, in _runFunc
00121:       return self._func(*self._args)
00122:     File "/net/apps/linux/scipion/1.2/pyworkflow/em/packages/xmipp3/protocol_resolution_monogenic_signal.py", line 252, in resolutionMonogenicSignalStep
00123:       self.runJob('xmipp_resolution_monogenic_signal', params)
00124:     File "/net/apps/linux/scipion/1.2/pyworkflow/protocol/protocol.py", line 1138, in runJob
00125:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00126:     File "/net/apps/linux/scipion/1.2/pyworkflow/protocol/executor.py", line 56, in runJob
00127:       env=env, cwd=cwd)
00128:     File "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 51, in runJob
00129:       return runCommand(command, env, cwd)
00130:     File "/net/apps/linux/scipion/1.2/pyworkflow/utils/process.py", line 65, in runCommand
00131:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd)
00132:     File "/net/apps/linux/scipion/1.2/software/lib/python2.7/subprocess.py", line 186, in check_call
00133:       raise CalledProcessError(retcode, cmd)
00134:   CalledProcessError: Command 'xmipp_resolution_monogenic_signal  --vol Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2 Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask Runs/000501_ProtImportMask/extra/mask.mrc --mask_out Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes 5.000000 --volumeRadius 160.000000 --chimera_volume Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i --significance 0.950000 --md_outputdata Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume ' returned non-zero exit status 139
00135:   Protocol failed: Command 'xmipp_resolution_monogenic_signal  --vol Runs/000421_ProtImportVolumes/extra/half2.mrc:mrc --vol2 Runs/000461_ProtImportVolumes/extra/half1.mrc:mrc --meanVol Runs/000535_XmippProtMonoRes/extra/mean_volume.vol --mask Runs/000501_ProtImportMask/extra/mask.mrc --mask_out Runs/000535_XmippProtMonoRes/extra/output_Mask.vol -o Runs/000535_XmippProtMonoRes/extra/mgresolution.vol --sampling_rate 1.297500 --number_frequencies 50.000000 --minRes 2.000000 --maxRes 5.000000 --volumeRadius 160.000000 --chimera_volume Runs/000535_XmippProtMonoRes/extra/MG_Chimera_resolution.vol --sym i --significance 0.950000 --md_outputdata Runs/000535_XmippProtMonoRes/extra/mask_data.xmd --filtered_volume ' returned non-zero exit status 139
00136:   FAILED: resolutionMonogenicSignalStep, step 2


Thanks,

Chen

Re: [scipion-users] Streaming/On-the-Fly processing

[Jose M. de la R. T. <del...@gm...>]

Hi Tim,

Thanks for your feedback. Below some answers.

On Mon, Jul 16, 2018 at 10:41 PM David Timm <dav...@bi...>
wrote:

> Hello, Sorry in advance for the long email.
>
> After watching the recent SBGrid video on Streaming in Scipion (
> https://www.youtube.com/watch?v=5fLrZ2BYJ28), I tried testing streaming
> processing with v1.2 (2018-04-02) Caligula.
>
> The 'scipion demo' worked fine with this version (as described
> https://github.com/I2PC/scipion/wiki/Streaming-Processing).
>
> I next transferred 20 apoferritin movies one at a time to a processing
> directory over a 100 minute time period (5 min between each movie). Several
> movies transferred before I started streaming importing in scipion.
>
> The Protocols SPA Protocol: scipion - import movies worked fine and
> contained a Streaming tab selected yes with 600 sec time out and 30 sec
> File timeout. Run mode continue was also selected. Started 15:47:41...
> Finished: 17:18:19...
>
> Next, I executed the motioncorr Protocol (Protocols SPA, motioncor2). Run
> mode Continue, no Streaming tab available, never the less all 20 movies got
> motion corrected in a streaming manner. Started 15:51:40 ... Finished:
> 17:18:21...
>
In version 1.2 motioncor2 is can run in streaming mode, but there are some
new features (Streaming Tab) that are introduced in the upcoming release
1.2.1. You can take a look at the upcoming changes here:
https://github.com/I2PC/scipion/wiki/Release-notes-v1.2.1-(2018-07-x) (it
is still an early draft of the Release Notes)

Likewise, the gctf Protocol (Protocols SPA) has no Streaming tab available
> but appeared to stream just fine with one potential issue that _psdFile
> column (Analyze Results) shows half image with calc'd FFT from fit CTF, but
> half where observed FFT should be appears black. Started 16:02:44...
> Finished 17:18:22...
>
Streaming tab in v1.2.1, there are a couple parameters there that could be
useful: batch size (process many items in one step, previously one
movie/mic = one step and waiting time...nice for fast protocols to stay
inactive (not consuming resources) and then wake up and process many items
at once).

>
> The motioncor2 and gctf outputs are consistent with results I've
> previously obtained via command line.
>
> ***QUESTION: Why is the observed FFT black, while the fit CTF in the
> analyze results table shows up just fine?***
>
Can you provide some images and more information about this? It is
difficult to figure out the problem with the given information.

>
> I also included a relion - auto-picking protocol, again no Streaming tab
> was present in the Protocols SPA protocol. This appeared to get off to a
> decent start, but in the end only the first 11 aligned micrographs got
> picked (Analyze Results: State = Manual), no particles were picked for the
> last 9 mics (State = Available). Started 16:17:21...  Finished 17:18:25...
> run.stderr is empty. I've attached run.stdout herein, all the autopicks
> including and beyond 'Picking micrograph:
> Runs/000079_ProtMotionCorr/extra/May08_05.55.31_aligned_mic_DW.mrc ' show 0
> Particles and State = Available in Analyze Results table. All but one of
> these micrographs autopick reasonably well using relion via command line
> with identical input parameters.
>

Picking was not completely working in that version in streaming. In 1.2.1
it will be and many more picking algorithms, plus extraction and scheduling
of 2D classification.

>
> ***QUESTION: Any ideas why the final 9 micrographs did not yield any
> autopicked particles and what does Available mean on the Analyze Results
> State column?***
>
> Thank you! Dave Timm
>
Kind regards,
Jose Miguel


>
> =======================================
> David E. Timm
> Electron Microscopy Core Laboratory
> Department of Biochemistry
> Crocker Science Center, room 038
> University of Utah
> Salt Lake City, Utah 84112 USA
> Phone  801.587.0353
> FAX  801.587.3077
> dav...@bi...
> =======================================
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Streaming/On-the-Fly processing

[David T. <dav...@bi...>]

Hello, Sorry in advance for the long email.

After watching the recent SBGrid video on Streaming in Scipion (https://www.youtube.com/watch?v=5fLrZ2BYJ28), I tried testing streaming processing with v1.2 (2018-04-02) Caligula.

The 'scipion demo' worked fine with this version (as described https://github.com/I2PC/scipion/wiki/Streaming-Processing).

I next transferred 20 apoferritin movies one at a time to a processing directory over a 100 minute time period (5 min between each movie). Several movies transferred before I started streaming importing in scipion.

The Protocols SPA Protocol: scipion - import movies worked fine and contained a Streaming tab selected yes with 600 sec time out and 30 sec File timeout. Run mode continue was also selected. Started 15:47:41... Finished: 17:18:19...

Next, I executed the motioncorr Protocol (Protocols SPA, motioncor2). Run mode Continue, no Streaming tab available, never the less all 20 movies got motion corrected in a streaming manner. Started 15:51:40 ... Finished: 17:18:21...

Likewise, the gctf Protocol (Protocols SPA) has no Streaming tab available but appeared to stream just fine with one potential issue that _psdFile column (Analyze Results) shows half image with calc'd FFT from fit CTF, but half where observed FFT should be appears black. Started 16:02:44... Finished 17:18:22...

The motioncor2 and gctf outputs are consistent with results I've previously obtained via command line.

***QUESTION: Why is the observed FFT black, while the fit CTF in the analyze results table shows up just fine?***

I also included a relion - auto-picking protocol, again no Streaming tab was present in the Protocols SPA protocol. This appeared to get off to a decent start, but in the end only the first 11 aligned micrographs got picked (Analyze Results: State = Manual), no particles were picked for the last 9 mics (State = Available). Started 16:17:21...  Finished 17:18:25... run.stderr is empty. I've attached run.stdout herein, all the autopicks including and beyond 'Picking micrograph: Runs/000079_ProtMotionCorr/extra/May08_05.55.31_aligned_mic_DW.mrc ' show 0 Particles and State = Available in Analyze Results table. All but one of these micrographs autopick reasonably well using relion via command line with identical input parameters.

***QUESTION: Any ideas why the final 9 micrographs did not yield any autopicked particles and what does Available mean on the Analyze Results State column?***

Thank you! Dave Timm

=======================================
David E. Timm
Electron Microscopy Core Laboratory
Department of Biochemistry
Crocker Science Center, room 038
University of Utah
Salt Lake City, Utah 84112 USA
Phone  801.587.0353
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dav...@bi...
=======================================

Re: [scipion-users] Xmipp viewer issue

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

Hi Erik,

You are editing the wrong file, you should check the ~/.
config/scipion/scipion.conf. It should contain
RELION_HOME=%(EM_ROOT)s/relion-1.4

Did you install relion through scipion or separately? If it was installed
separately, relion-1.4 link should point to relion installation folder.
Also, have you tried to run relion outside of Scipion?


On Fri, Jul 13, 2018, 10:10 Erik Župa <eri...@gm...> wrote:

> Thanks for advice but I have already tried this thing and it is not
> working. I tried  to use RELION_HOME=%(EM_ROOT)s/relion-1.4, I also tried
> the write whole pathway RELION_HOME =
> /home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/relion-1.4
> but the result is same. If I try to run configuration of Scipion with both
> cases I get this  "In section BUILD, option RELION_HOME exists in the
> configuration file but not in the template."
>
>
> Erik Zupa
>
> On Thu, Jul 12, 2018 at 2:07 PM, Gregory Sharov <sha...@gm...>
> wrote:
>
>> In ~/.config/scipion/scipion.conf there is a line pointing to scipion
>> EM_ROOT folder (you should adjust version name to the one you have), i.e.:
>> RELION_HOME=%(EM_ROOT)s/relion-1.4
>>
>> It points to scipion/software/em/relion-1.4 which could be a symbolic
>> link to whatever path you have installed relion.
>>
>> Please have a look at
>> https://github.com/I2PC/scipion/wiki/Installing-EM-Packages#linking-to-existing-package-installations
>>
>> 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 267542
>> e-mail: gs...@mr...
>>
>>
>> On Thu, Jul 12, 2018 at 1:01 PM Erik Župa <eri...@gm...> wrote:
>>
>>> My config file is totally missing RELION_HOME despite the relion package
>>> was installed. How do I set RELION_HOME?
>>>
>>> Erik Zupa
>>>
>>> On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <
>>> sha...@gm...> wrote:
>>>
>>>> Hi Erik,
>>>>
>>>> It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
>>>> correct RELION_HOME set in config file? Did you try running relion with mpi
>>>> outside of scipion?
>>>>
>>>> On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:
>>>>
>>>>> I solved the problem of particle extraction window. It was wrong Java
>>>>> path. However, my relion 2D classification is not working, Scipion is
>>>>> showing  this Error
>>>>>
>>>>> Erik Zupa
>>>>>
>>>>> 00021:   mpirun: Error: unknown option "--tau2_fudge"
>>>>> 00022:   Type 'mpirun --help' for usage.
>>>>> 00023:   Traceback (most recent call last):
>>>>> 00024:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>>>> line 182, in run
>>>>> 00025:       self._run()
>>>>> 00026:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>>>> line 228, in _run
>>>>> 00027:       resultFiles = self._runFunc()
>>>>> 00028:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>>>> line 224, in _runFunc
>>>>> 00029:       return self._func(*self._args)
>>>>> 00030:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
>>>>> line 789, in runRelionStep
>>>>> 00031:       self.runJob(self._getProgram(), params)
>>>>> 00032:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>>>> line 1077, in runJob
>>>>> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
>>>>> **kwargs)
>>>>> 00034:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
>>>>> line 56, in runJob
>>>>> 00035:       env=env, cwd=cwd)
>>>>> 00036:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>>>> line 51, in runJob
>>>>> 00037:       return runCommand(command, env, cwd)
>>>>> 00038:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>>>> line 65, in runCommand
>>>>> 00039:       check_call(command, shell=True, stdout=sys.stdout,
>>>>> stderr=sys.stderr, env=env, cwd=cwd)
>>>>> 00040:     File
>>>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
>>>>> line 540, in check_call
>>>>> 00041:       raise CalledProcessError(retcode, cmd)
>>>>> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
>>>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>>>> status 213
>>>>> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
>>>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>>>> status 213
>>>>>
>>>>> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
>>>>> wrote:
>>>>>
>>>>>> is java in your path?
>>>>>>
>>>>>> what happens if you type in the "console/terminal":
>>>>>>
>>>>>> java -version
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 09/07/18 14:39, David Maluenda wrote:
>>>>>>
>>>>>> Ouch.. strange..
>>>>>>
>>>>>> What appears as Output for the Xmipp-ExtractParticles? Could the
>>>>>> output set be empty?
>>>>>> The summary tab (in the scipion GUI) should display:
>>>>>>
>>>>>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (*
>>>>>> # items*, ** x **, **.* A/px )
>>>>>>
>>>>>> Then, the number of items # is bigger than 0?
>>>>>>
>>>>>> ​ <http://ucm.es/>
>>>>>>
>>>>>> *_____ Dr. David Maluenda Niubó*
>>>>>> dma...@cn... - (+34) 619 029 310
>>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>>
>>>>>> This email message and any documents attached to it may contain
>>>>>> confidential or legally protected material and are intended solely for the
>>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>>> you that if you are not the intended recipient of this email message or the
>>>>>> person responsible for processing it, then you are not authorized to read,
>>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>>> sender of this and to eliminate both the message and any attachments it
>>>>>> carries from your account. Thank you for your collaboration.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>>>>>
>>>>>>> Hi David,
>>>>>>>
>>>>>>> I am not receiving any error messages from Scipion after the
>>>>>>> command. However, there is no new window popping out after the command.
>>>>>>>
>>>>>>> Erik Zupa
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <
>>>>>>> dma...@cn...> wrote:
>>>>>>>
>>>>>>>> Hi Erik,
>>>>>>>>
>>>>>>>> This is the command that Scipion launch to open the viewer and it
>>>>>>>> looks fine.. so, it should open a window with the particles...
>>>>>>>>
>>>>>>>> Is there any error message after the command that you are reporting?
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> ​ <http://ucm.es/>
>>>>>>>>
>>>>>>>> *_____ Dr. David Maluenda Niubó*
>>>>>>>> dma...@cn... - (+34) 619 029 310
>>>>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>>>>
>>>>>>>> This email message and any documents attached to it may contain
>>>>>>>> confidential or legally protected material and are intended solely for the
>>>>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>>>>> you that if you are not the intended recipient of this email message or the
>>>>>>>> person responsible for processing it, then you are not authorized to read,
>>>>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>>>>> sender of this and to eliminate both the message and any attachments it
>>>>>>>> carries from your account. Thank you for your collaboration.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hello colleagues,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I have problem to analyze results of extracting of particles. I
>>>>>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>>>>>> results because everytime I try, Scipion come with something like this:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> java -Xmx2g -d64
>>>>>>>>> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
>>>>>>>>> -cp
>>>>>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>>>>>> xmipp.viewer.scipion.ScipionViewer -i
>>>>>>>>> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id
>>>>>>>>> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I am thankful for any help.
>>>>>>>>>
>>>>>>>>> Erik Zupa
>>>>>>>>>
>>>>>>>>> CEITEC Brno Czech Republic
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>>>> _______________________________________________
>>>>>>>>> scipion-users mailing list
>>>>>>>>> sci...@li...
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> scipion-users mailing list
>>>>>> sci...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Xmipp viewer issue

[Erik Ž. <eri...@gm...>]

Thanks for advice but I have already tried this thing and it is not
working. I tried  to use RELION_HOME=%(EM_ROOT)s/relion-1.4, I also tried
the write whole pathway RELION_HOME =
/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/relion-1.4
but the result is same. If I try to run configuration of Scipion with both
cases I get this  "In section BUILD, option RELION_HOME exists in the
configuration file but not in the template."


Erik Zupa

On Thu, Jul 12, 2018 at 2:07 PM, Gregory Sharov <sha...@gm...>
wrote:

> In ~/.config/scipion/scipion.conf there is a line pointing to scipion
> EM_ROOT folder (you should adjust version name to the one you have), i.e.:
> RELION_HOME=%(EM_ROOT)s/relion-1.4
>
> It points to scipion/software/em/relion-1.4 which could be a symbolic link
> to whatever path you have installed relion.
>
> Please have a look at https://github.com/I2PC/scipion/wiki/Installing-EM-
> Packages#linking-to-existing-package-installations
>
> 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 267542
> e-mail: gs...@mr...
>
>
> On Thu, Jul 12, 2018 at 1:01 PM Erik Župa <eri...@gm...> wrote:
>
>> My config file is totally missing RELION_HOME despite the relion package
>> was installed. How do I set RELION_HOME?
>>
>> Erik Zupa
>>
>> On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <sha...@gm...
>> > wrote:
>>
>>> Hi Erik,
>>>
>>> It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
>>> correct RELION_HOME set in config file? Did you try running relion with mpi
>>> outside of scipion?
>>>
>>> On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:
>>>
>>>> I solved the problem of particle extraction window. It was wrong Java
>>>> path. However, my relion 2D classification is not working, Scipion is
>>>> showing  this Error
>>>>
>>>> Erik Zupa
>>>>
>>>> 00021:   mpirun: Error: unknown option "--tau2_fudge"
>>>> 00022:   Type 'mpirun --help' for usage.
>>>> 00023:   Traceback (most recent call last):
>>>> 00024:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/protocol/protocol.py", line 182, in run
>>>> 00025:       self._run()
>>>> 00026:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/protocol/protocol.py", line 228, in _run
>>>> 00027:       resultFiles = self._runFunc()
>>>> 00028:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/protocol/protocol.py", line 224, in _runFunc
>>>> 00029:       return self._func(*self._args)
>>>> 00030:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py", line
>>>> 789, in runRelionStep
>>>> 00031:       self.runJob(self._getProgram(), params)
>>>> 00032:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/protocol/protocol.py", line 1077, in runJob
>>>> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
>>>> **kwargs)
>>>> 00034:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/protocol/executor.py", line 56, in runJob
>>>> 00035:       env=env, cwd=cwd)
>>>> 00036:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/utils/process.py", line 51, in runJob
>>>> 00037:       return runCommand(command, env, cwd)
>>>> 00038:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/pyworkflow/utils/process.py", line 65, in runCommand
>>>> 00039:       check_call(command, shell=True, stdout=sys.stdout,
>>>> stderr=sys.stderr, env=env, cwd=cwd)
>>>> 00040:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>>>> linux64/scipion/software/lib/python2.7/subprocess.py", line 540, in
>>>> check_call
>>>> 00041:       raise CalledProcessError(retcode, cmd)
>>>> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
>>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>>> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_
>>>> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0
>>>> --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent  --zero_mask
>>>> --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit status 213
>>>> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
>>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>>> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_
>>>> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0
>>>> --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent  --zero_mask
>>>> --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit status 213
>>>>
>>>> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
>>>> wrote:
>>>>
>>>>> is java in your path?
>>>>>
>>>>> what happens if you type in the "console/terminal":
>>>>>
>>>>> java -version
>>>>>
>>>>>
>>>>>
>>>>> On 09/07/18 14:39, David Maluenda wrote:
>>>>>
>>>>> Ouch.. strange..
>>>>>
>>>>> What appears as Output for the Xmipp-ExtractParticles? Could the
>>>>> output set be empty?
>>>>> The summary tab (in the scipion GUI) should display:
>>>>>
>>>>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (*
>>>>> # items*, ** x **, **.* A/px )
>>>>>
>>>>> Then, the number of items # is bigger than 0?
>>>>>
>>>>> ​ <http://ucm.es/>
>>>>>
>>>>> *_____ Dr. David Maluenda Niubó*
>>>>> dma...@cn... - (+34) 619 029 310
>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>
>>>>> This email message and any documents attached to it may contain
>>>>> confidential or legally protected material and are intended solely for the
>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>> you that if you are not the intended recipient of this email message or the
>>>>> person responsible for processing it, then you are not authorized to read,
>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>> sender of this and to eliminate both the message and any attachments it
>>>>> carries from your account. Thank you for your collaboration.
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> I am not receiving any error messages from Scipion after the command.
>>>>>> However, there is no new window popping out after the command.
>>>>>>
>>>>>> Erik Zupa
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <
>>>>>> dma...@cn...> wrote:
>>>>>>
>>>>>>> Hi Erik,
>>>>>>>
>>>>>>> This is the command that Scipion launch to open the viewer and it
>>>>>>> looks fine.. so, it should open a window with the particles...
>>>>>>>
>>>>>>> Is there any error message after the command that you are reporting?
>>>>>>>
>>>>>>> Thanks!
>>>>>>>
>>>>>>> ​ <http://ucm.es/>
>>>>>>>
>>>>>>> *_____ Dr. David Maluenda Niubó*
>>>>>>> dma...@cn... - (+34) 619 029 310
>>>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>>>
>>>>>>> This email message and any documents attached to it may contain
>>>>>>> confidential or legally protected material and are intended solely for the
>>>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>>>> you that if you are not the intended recipient of this email message or the
>>>>>>> person responsible for processing it, then you are not authorized to read,
>>>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>>>> sender of this and to eliminate both the message and any attachments it
>>>>>>> carries from your account. Thank you for your collaboration.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hello colleagues,
>>>>>>>>
>>>>>>>>
>>>>>>>> I have problem to analyze results of extracting of particles. I
>>>>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>>>>> results because everytime I try, Scipion come with something like this:
>>>>>>>>
>>>>>>>>
>>>>>>>> java -Xmx2g -d64 -Djava.library.path=/home/
>>>>>>>> erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>>>> 06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
>>>>>>>> -cp /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.
>>>>>>>> x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>>>> 06-14_linux64/scipion/software/em/xmipp/external/
>>>>>>>> imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>>>> 06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>>>>> xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_
>>>>>>>> XmippProtExtractParticles/particles.sqlite" --visible id enabled
>>>>>>>> _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>>>>
>>>>>>>>
>>>>>>>> I am thankful for any help.
>>>>>>>>
>>>>>>>> Erik Zupa
>>>>>>>>
>>>>>>>> CEITEC Brno Czech Republic
>>>>>>>> ------------------------------------------------------------
>>>>>>>> ------------------
>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>>>>>> _________________________________________
>>>>>>>> scipion-users mailing list
>>>>>>>> sci...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
>>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>> _________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] Xmipp viewer issue

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

In ~/.config/scipion/scipion.conf there is a line pointing to scipion
EM_ROOT folder (you should adjust version name to the one you have), i.e.:
RELION_HOME=%(EM_ROOT)s/relion-1.4

It points to scipion/software/em/relion-1.4 which could be a symbolic link
to whatever path you have installed relion.

Please have a look at
https://github.com/I2PC/scipion/wiki/Installing-EM-Packages#linking-to-existing-package-installations

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 267542
e-mail: gs...@mr...


On Thu, Jul 12, 2018 at 1:01 PM Erik Župa <eri...@gm...> wrote:

> My config file is totally missing RELION_HOME despite the relion package
> was installed. How do I set RELION_HOME?
>
> Erik Zupa
>
> On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <sha...@gm...>
> wrote:
>
>> Hi Erik,
>>
>> It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
>> correct RELION_HOME set in config file? Did you try running relion with mpi
>> outside of scipion?
>>
>> On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:
>>
>>> I solved the problem of particle extraction window. It was wrong Java
>>> path. However, my relion 2D classification is not working, Scipion is
>>> showing  this Error
>>>
>>> Erik Zupa
>>>
>>> 00021:   mpirun: Error: unknown option "--tau2_fudge"
>>> 00022:   Type 'mpirun --help' for usage.
>>> 00023:   Traceback (most recent call last):
>>> 00024:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 182, in run
>>> 00025:       self._run()
>>> 00026:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 228, in _run
>>> 00027:       resultFiles = self._runFunc()
>>> 00028:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 224, in _runFunc
>>> 00029:       return self._func(*self._args)
>>> 00030:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
>>> line 789, in runRelionStep
>>> 00031:       self.runJob(self._getProgram(), params)
>>> 00032:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 1077, in runJob
>>> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
>>> **kwargs)
>>> 00034:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
>>> line 56, in runJob
>>> 00035:       env=env, cwd=cwd)
>>> 00036:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>> line 51, in runJob
>>> 00037:       return runCommand(command, env, cwd)
>>> 00038:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>> line 65, in runCommand
>>> 00039:       check_call(command, shell=True, stdout=sys.stdout,
>>> stderr=sys.stderr, env=env, cwd=cwd)
>>> 00040:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
>>> line 540, in check_call
>>> 00041:       raise CalledProcessError(retcode, cmd)
>>> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>> status 213
>>> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>> status 213
>>>
>>> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
>>> wrote:
>>>
>>>> is java in your path?
>>>>
>>>> what happens if you type in the "console/terminal":
>>>>
>>>> java -version
>>>>
>>>>
>>>>
>>>> On 09/07/18 14:39, David Maluenda wrote:
>>>>
>>>> Ouch.. strange..
>>>>
>>>> What appears as Output for the Xmipp-ExtractParticles? Could the output
>>>> set be empty?
>>>> The summary tab (in the scipion GUI) should display:
>>>>
>>>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (*
>>>> # items*, ** x **, **.* A/px )
>>>>
>>>> Then, the number of items # is bigger than 0?
>>>>
>>>> ​ <http://ucm.es/>
>>>>
>>>> *_____ Dr. David Maluenda Niubó*
>>>> dma...@cn... - (+34) 619 029 310
>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>
>>>> This email message and any documents attached to it may contain
>>>> confidential or legally protected material and are intended solely for the
>>>> use of the individual or organization to whom they are addressed. We remind
>>>> you that if you are not the intended recipient of this email message or the
>>>> person responsible for processing it, then you are not authorized to read,
>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>> received this email message by mistake, we kindly ask you to inform the
>>>> sender of this and to eliminate both the message and any attachments it
>>>> carries from your account. Thank you for your collaboration.
>>>>
>>>>
>>>>
>>>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>>>
>>>>> Hi David,
>>>>>
>>>>> I am not receiving any error messages from Scipion after the command.
>>>>> However, there is no new window popping out after the command.
>>>>>
>>>>> Erik Zupa
>>>>>
>>>>>
>>>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...
>>>>> > wrote:
>>>>>
>>>>>> Hi Erik,
>>>>>>
>>>>>> This is the command that Scipion launch to open the viewer and it
>>>>>> looks fine.. so, it should open a window with the particles...
>>>>>>
>>>>>> Is there any error message after the command that you are reporting?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> ​ <http://ucm.es/>
>>>>>>
>>>>>> *_____ Dr. David Maluenda Niubó*
>>>>>> dma...@cn... - (+34) 619 029 310
>>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>>
>>>>>> This email message and any documents attached to it may contain
>>>>>> confidential or legally protected material and are intended solely for the
>>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>>> you that if you are not the intended recipient of this email message or the
>>>>>> person responsible for processing it, then you are not authorized to read,
>>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>>> sender of this and to eliminate both the message and any attachments it
>>>>>> carries from your account. Thank you for your collaboration.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello colleagues,
>>>>>>>
>>>>>>>
>>>>>>> I have problem to analyze results of extracting of particles. I
>>>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>>>> results because everytime I try, Scipion come with something like this:
>>>>>>>
>>>>>>>
>>>>>>> java -Xmx2g -d64
>>>>>>> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
>>>>>>> -cp
>>>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>>>> xmipp.viewer.scipion.ScipionViewer -i
>>>>>>> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id
>>>>>>> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>>>
>>>>>>>
>>>>>>> I am thankful for any help.
>>>>>>>
>>>>>>> Erik Zupa
>>>>>>>
>>>>>>> CEITEC Brno Czech Republic
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>>> _______________________________________________
>>>>>>> scipion-users mailing list
>>>>>>> sci...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Xmipp viewer issue

[Erik Ž. <eri...@gm...>]

My config file is totally missing RELION_HOME despite the relion package
was installed. How do I set RELION_HOME?

Erik Zupa

On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <sha...@gm...>
wrote:

> Hi Erik,
>
> It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
> correct RELION_HOME set in config file? Did you try running relion with mpi
> outside of scipion?
>
> On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:
>
>> I solved the problem of particle extraction window. It was wrong Java
>> path. However, my relion 2D classification is not working, Scipion is
>> showing  this Error
>>
>> Erik Zupa
>>
>> 00021:   mpirun: Error: unknown option "--tau2_fudge"
>> 00022:   Type 'mpirun --help' for usage.
>> 00023:   Traceback (most recent call last):
>> 00024:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/protocol/protocol.py", line 182, in run
>> 00025:       self._run()
>> 00026:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/protocol/protocol.py", line 228, in _run
>> 00027:       resultFiles = self._runFunc()
>> 00028:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/protocol/protocol.py", line 224, in _runFunc
>> 00029:       return self._func(*self._args)
>> 00030:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py", line
>> 789, in runRelionStep
>> 00031:       self.runJob(self._getProgram(), params)
>> 00032:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/protocol/protocol.py", line 1077, in runJob
>> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
>> **kwargs)
>> 00034:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/protocol/executor.py", line 56, in runJob
>> 00035:       env=env, cwd=cwd)
>> 00036:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/utils/process.py", line 51, in runJob
>> 00037:       return runCommand(command, env, cwd)
>> 00038:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/pyworkflow/utils/process.py", line 65, in runCommand
>> 00039:       check_call(command, shell=True, stdout=sys.stdout,
>> stderr=sys.stderr, env=env, cwd=cwd)
>> 00040:     File "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_
>> linux64/scipion/software/lib/python2.7/subprocess.py", line 540, in
>> check_call
>> 00041:       raise CalledProcessError(retcode, cmd)
>> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_
>> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0 --K
>> 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent  --zero_mask
>> --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit status 213
>> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>> Runs/003210_ProtRelionClassify2D/extra/relion --i Runs/003210_
>> ProtRelionClassify2D/input_particles.star --particle_diameter 210.0 --K
>> 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent  --zero_mask
>> --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit status 213
>>
>> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
>> wrote:
>>
>>> is java in your path?
>>>
>>> what happens if you type in the "console/terminal":
>>>
>>> java -version
>>>
>>>
>>>
>>> On 09/07/18 14:39, David Maluenda wrote:
>>>
>>> Ouch.. strange..
>>>
>>> What appears as Output for the Xmipp-ExtractParticles? Could the output
>>> set be empty?
>>> The summary tab (in the scipion GUI) should display:
>>>
>>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (*
>>> # items*, ** x **, **.* A/px )
>>>
>>> Then, the number of items # is bigger than 0?
>>>
>>> ​ <http://ucm.es/>
>>>
>>> *_____ Dr. David Maluenda Niubó*
>>> dma...@cn... - (+34) 619 029 310
>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>> BioComputing Unit <http://biocomputingunit.es/>
>>>
>>> This email message and any documents attached to it may contain
>>> confidential or legally protected material and are intended solely for the
>>> use of the individual or organization to whom they are addressed. We remind
>>> you that if you are not the intended recipient of this email message or the
>>> person responsible for processing it, then you are not authorized to read,
>>> save, modify, send, copy or disclose any of its contents. If you have
>>> received this email message by mistake, we kindly ask you to inform the
>>> sender of this and to eliminate both the message and any attachments it
>>> carries from your account. Thank you for your collaboration.
>>>
>>>
>>>
>>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>>
>>>> Hi David,
>>>>
>>>> I am not receiving any error messages from Scipion after the command.
>>>> However, there is no new window popping out after the command.
>>>>
>>>> Erik Zupa
>>>>
>>>>
>>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...>
>>>> wrote:
>>>>
>>>>> Hi Erik,
>>>>>
>>>>> This is the command that Scipion launch to open the viewer and it
>>>>> looks fine.. so, it should open a window with the particles...
>>>>>
>>>>> Is there any error message after the command that you are reporting?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> ​ <http://ucm.es/>
>>>>>
>>>>> *_____ Dr. David Maluenda Niubó*
>>>>> dma...@cn... - (+34) 619 029 310
>>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>>
>>>>> This email message and any documents attached to it may contain
>>>>> confidential or legally protected material and are intended solely for the
>>>>> use of the individual or organization to whom they are addressed. We remind
>>>>> you that if you are not the intended recipient of this email message or the
>>>>> person responsible for processing it, then you are not authorized to read,
>>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>>> received this email message by mistake, we kindly ask you to inform the
>>>>> sender of this and to eliminate both the message and any attachments it
>>>>> carries from your account. Thank you for your collaboration.
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote:
>>>>>
>>>>>> Hello colleagues,
>>>>>>
>>>>>>
>>>>>> I have problem to analyze results of extracting of particles. I
>>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>>> results because everytime I try, Scipion come with something like this:
>>>>>>
>>>>>>
>>>>>> java -Xmx2g -d64 -Djava.library.path=/home/
>>>>>> erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>> 06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins -cp
>>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.
>>>>>> x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>> 06-14_linux64/scipion/software/em/xmipp/external/
>>>>>> imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>>>> 06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>>> xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_
>>>>>> XmippProtExtractParticles/particles.sqlite" --visible id enabled
>>>>>> _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>>
>>>>>>
>>>>>> I am thankful for any help.
>>>>>>
>>>>>> Erik Zupa
>>>>>>
>>>>>> CEITEC Brno Czech Republic
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>>>> _________________________________________
>>>>>> scipion-users mailing list
>>>>>> sci...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>>
>>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] Xmipp viewer issue

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

Hi Erik,

It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
correct RELION_HOME set in config file? Did you try running relion with mpi
outside of scipion?

On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:

> I solved the problem of particle extraction window. It was wrong Java
> path. However, my relion 2D classification is not working, Scipion is
> showing  this Error
>
> Erik Zupa
>
> 00021:   mpirun: Error: unknown option "--tau2_fudge"
> 00022:   Type 'mpirun --help' for usage.
> 00023:   Traceback (most recent call last):
> 00024:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 182, in run
> 00025:       self._run()
> 00026:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 228, in _run
> 00027:       resultFiles = self._runFunc()
> 00028:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 224, in _runFunc
> 00029:       return self._func(*self._args)
> 00030:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
> line 789, in runRelionStep
> 00031:       self.runJob(self._getProgram(), params)
> 00032:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
> line 1077, in runJob
> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
> 00034:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
> line 56, in runJob
> 00035:       env=env, cwd=cwd)
> 00036:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
> line 51, in runJob
> 00037:       return runCommand(command, env, cwd)
> 00038:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
> line 65, in runCommand
> 00039:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr, env=env, cwd=cwd)
> 00040:     File
> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
> line 540, in check_call
> 00041:       raise CalledProcessError(retcode, cmd)
> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
> Runs/003210_ProtRelionClassify2D/extra/relion --i
> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
> status 213
> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
> Runs/003210_ProtRelionClassify2D/extra/relion --i
> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
> status 213
>
> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
> wrote:
>
>> is java in your path?
>>
>> what happens if you type in the "console/terminal":
>>
>> java -version
>>
>>
>>
>> On 09/07/18 14:39, David Maluenda wrote:
>>
>> Ouch.. strange..
>>
>> What appears as Output for the Xmipp-ExtractParticles? Could the output
>> set be empty?
>> The summary tab (in the scipion GUI) should display:
>>
>> *Name-of-the-protocol* -> outputParticles            SetOfParticles (* #
>> items*, ** x **, **.* A/px )
>>
>> Then, the number of items # is bigger than 0?
>>
>> ​ <http://ucm.es/>
>>
>> *_____ Dr. David Maluenda Niubó*
>> dma...@cn... - (+34) 619 029 310
>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>> BioComputing Unit <http://biocomputingunit.es/>
>>
>> This email message and any documents attached to it may contain
>> confidential or legally protected material and are intended solely for the
>> use of the individual or organization to whom they are addressed. We remind
>> you that if you are not the intended recipient of this email message or the
>> person responsible for processing it, then you are not authorized to read,
>> save, modify, send, copy or disclose any of its contents. If you have
>> received this email message by mistake, we kindly ask you to inform the
>> sender of this and to eliminate both the message and any attachments it
>> carries from your account. Thank you for your collaboration.
>>
>>
>>
>> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>>
>>> Hi David,
>>>
>>> I am not receiving any error messages from Scipion after the command.
>>> However, there is no new window popping out after the command.
>>>
>>> Erik Zupa
>>>
>>>
>>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...>
>>> wrote:
>>>
>>>> Hi Erik,
>>>>
>>>> This is the command that Scipion launch to open the viewer and it looks
>>>> fine.. so, it should open a window with the particles...
>>>>
>>>> Is there any error message after the command that you are reporting?
>>>>
>>>> Thanks!
>>>>
>>>> ​ <http://ucm.es/>
>>>>
>>>> *_____ Dr. David Maluenda Niubó*
>>>> dma...@cn... - (+34) 619 029 310
>>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>>> BioComputing Unit <http://biocomputingunit.es/>
>>>>
>>>> This email message and any documents attached to it may contain
>>>> confidential or legally protected material and are intended solely for the
>>>> use of the individual or organization to whom they are addressed. We remind
>>>> you that if you are not the intended recipient of this email message or the
>>>> person responsible for processing it, then you are not authorized to read,
>>>> save, modify, send, copy or disclose any of its contents. If you have
>>>> received this email message by mistake, we kindly ask you to inform the
>>>> sender of this and to eliminate both the message and any attachments it
>>>> carries from your account. Thank you for your collaboration.
>>>>
>>>>
>>>>
>>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote:
>>>>
>>>>> Hello colleagues,
>>>>>
>>>>>
>>>>> I have problem to analyze results of extracting of particles. I
>>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>>> results because everytime I try, Scipion come with something like this:
>>>>>
>>>>>
>>>>> java -Xmx2g -d64
>>>>> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
>>>>> -cp
>>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>>> xmipp.viewer.scipion.ScipionViewer -i
>>>>> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id
>>>>> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>>
>>>>>
>>>>> I am thankful for any help.
>>>>>
>>>>> Erik Zupa
>>>>>
>>>>> CEITEC Brno Czech Republic
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> scipion-users mailing list
>>>>> sci...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>>
>>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Xmipp viewer issue

[Erik Ž. <eri...@gm...>]

I solved the problem of particle extraction window. It was wrong Java path.
However, my relion 2D classification is not working, Scipion is showing
this Error

Erik Zupa

00021:   mpirun: Error: unknown option "--tau2_fudge"
00022:   Type 'mpirun --help' for usage.
00023:   Traceback (most recent call last):
00024:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
line 182, in run
00025:       self._run()
00026:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
line 228, in _run
00027:       resultFiles = self._runFunc()
00028:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
line 224, in _runFunc
00029:       return self._func(*self._args)
00030:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
line 789, in runRelionStep
00031:       self.runJob(self._getProgram(), params)
00032:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
line 1077, in runJob
00033:       self._stepsExecutor.runJob(self._log, program, arguments,
**kwargs)
00034:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
line 56, in runJob
00035:       env=env, cwd=cwd)
00036:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
line 51, in runJob
00037:       return runCommand(command, env, cwd)
00038:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
line 65, in runCommand
00039:       check_call(command, shell=True, stdout=sys.stdout,
stderr=sys.stderr, env=env, cwd=cwd)
00040:     File
"/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
line 540, in check_call
00041:       raise CalledProcessError(retcode, cmd)
00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
--memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
Runs/003210_ProtRelionClassify2D/extra/relion --i
Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
--zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
status 213
00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
--memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
Runs/003210_ProtRelionClassify2D/extra/relion --i
Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
--zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
status 213

On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...> wrote:

> is java in your path?
>
> what happens if you type in the "console/terminal":
>
> java -version
>
>
>
> On 09/07/18 14:39, David Maluenda wrote:
>
> Ouch.. strange..
>
> What appears as Output for the Xmipp-ExtractParticles? Could the output
> set be empty?
> The summary tab (in the scipion GUI) should display:
>
> *Name-of-the-protocol* -> outputParticles            SetOfParticles (* #
> items*, ** x **, **.* A/px )
>
> Then, the number of items # is bigger than 0?
>
> ​ <http://ucm.es/>
>
> *_____ Dr. David Maluenda Niubó*
> dma...@cn... - (+34) 619 029 310
> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
> BioComputing Unit <http://biocomputingunit.es/>
>
> This email message and any documents attached to it may contain
> confidential or legally protected material and are intended solely for the
> use of the individual or organization to whom they are addressed. We remind
> you that if you are not the intended recipient of this email message or the
> person responsible for processing it, then you are not authorized to read,
> save, modify, send, copy or disclose any of its contents. If you have
> received this email message by mistake, we kindly ask you to inform the
> sender of this and to eliminate both the message and any attachments it
> carries from your account. Thank you for your collaboration.
>
>
>
> On Mon, Jul 9, 2018 at 1:23 PM Erik Župa <eri...@gm...> wrote:
>
>> Hi David,
>>
>> I am not receiving any error messages from Scipion after the command.
>> However, there is no new window popping out after the command.
>>
>> Erik Zupa
>>
>>
>> On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...>
>> wrote:
>>
>>> Hi Erik,
>>>
>>> This is the command that Scipion launch to open the viewer and it looks
>>> fine.. so, it should open a window with the particles...
>>>
>>> Is there any error message after the command that you are reporting?
>>>
>>> Thanks!
>>>
>>> ​ <http://ucm.es/>
>>>
>>> *_____ Dr. David Maluenda Niubó*
>>> dma...@cn... - (+34) 619 029 310
>>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>>> BioComputing Unit <http://biocomputingunit.es/>
>>>
>>> This email message and any documents attached to it may contain
>>> confidential or legally protected material and are intended solely for the
>>> use of the individual or organization to whom they are addressed. We remind
>>> you that if you are not the intended recipient of this email message or the
>>> person responsible for processing it, then you are not authorized to read,
>>> save, modify, send, copy or disclose any of its contents. If you have
>>> received this email message by mistake, we kindly ask you to inform the
>>> sender of this and to eliminate both the message and any attachments it
>>> carries from your account. Thank you for your collaboration.
>>>
>>>
>>>
>>> On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote:
>>>
>>>> Hello colleagues,
>>>>
>>>>
>>>> I have problem to analyze results of extracting of particles. I
>>>> successfully ran xmipp3- extract particles. However, I cannot analyze
>>>> results because everytime I try, Scipion come with something like this:
>>>>
>>>>
>>>> java -Xmx2g -d64 -Djava.library.path=/home/
>>>> erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
>>>> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>> 06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins -cp
>>>> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.
>>>> x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>> 06-14_linux64/scipion/software/em/xmipp/external/
>>>> imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-
>>>> 06-14_linux64/scipion/software/em/xmipp/java/lib/*
>>>> xmipp.viewer.scipion.ScipionViewer -i "Runs/002809_
>>>> XmippProtExtractParticles/particles.sqlite" --visible id enabled
>>>> _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
>>>> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
>>>> _transform._matrix --order id enabled _index _filename _xmipp_zScore
>>>> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
>>>> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
>>>> _xmipp_zScore asc --scipion 55971 2856
>>>>
>>>>
>>>> I am thankful for any help.
>>>>
>>>> Erik Zupa
>>>>
>>>> CEITEC Brno Czech Republic
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>>> _________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>