scipion-users — Mailing list for Scipion users

Re: [scipion-users] Metadata loading

[Сергей Н. <ser...@un...>]

Thank you Jose,

If you need any other data/files etc., just let me know.

Best,
Sergey

2016-09-29 10:21 GMT+02:00 Jose Miguel de la Rosa Trevin <
del...@gm...>:

> Thanks Sergey,
>
> I think that you should split that into different projects if it is really
> another project. If it is the same one, it make sense to add to the current
> one. But this would be a way to alleviate the current issue. We will let
> you know about any progress related this. Thanks a lot for sharing the
> project.sqlite database for further inspection.
>
> Cheers,
> Jose Miguel.
>
>
>
> On Thu, Sep 29, 2016 at 10:17 AM, Сергей Назаров <ser...@un...
> > wrote:
>
>> Dear Jose, Pablo,
>>
>> Here is the project file, I also attach settings file just in case.
>> Yes, the tree is really big, I simply add branches as soon is new data is
>> arriving. So, for future I would try to split the data into as many
>> projects as possible.
>>
>> Best,
>> Sergey
>>
>> 2016-09-28 11:23 GMT+02:00 Jose Miguel de la Rosa Trevin <
>> del...@gm...>:
>>
>>> Dear Serguey,
>>>
>>> As Pablo said, thanks for given us important feedback. Could you share
>>> you project.sqlite databaset with us? So we can perform some tests on it.
>>> It should work with this number of runs and this would be smother after we
>>> fix some refresh problems.
>>>
>>> Kind regards,
>>> Jose Miguel.
>>>
>>>
>>> On Wed, Sep 28, 2016 at 11:00 AM, Pablo <p.c...@gm...>
>>> wrote:
>>>
>>>> Wow! We certainly need to have your case in mind (589 runs) when
>>>> testing performance.
>>>> Collapsing some branches actually reduce "drawing time" but the whole
>>>> project is loaded which takes most of the time.
>>>>
>>>> Now I can't see any other workaround than deleting runs. If you want to
>>>> keep them all, another option could be to copy the project folder (watch
>>>> out for the disk space), and in the new project delete runs.
>>>> But I can understand this way you loose the whole picture of the
>>>> project.
>>>>
>>>> I've added your case into our issue, and will discuss your case in our
>>>> next development meeting.
>>>>
>>>> :-(
>>>>
>>>> Pablo.
>>>>
>>>>
>>>> On 27/09/16 16:26, Сергей Назаров wrote:
>>>>
>>>> Dear Pablo,
>>>>
>>>> Thank you for a quick reply. Unfortunately, I don't have many protocols
>>>> running at the same time, usually from 1 to 3. But the project is huge, the
>>>> number of folders in Runs/ is 589. I keep most of branches collapsed,
>>>> hopefully it prevent them from loading.
>>>>
>>>> Best,
>>>> Sergey
>>>>
>>>> 2016-09-26 19:00 GMT+02:00 Pablo <p.c...@gm...>:
>>>>
>>>>> Dear Sergey,
>>>>>
>>>>> Thanks a lot for your feedback, this is very important for us to know
>>>>> important issues and also to give priority to new features. We are aware of
>>>>> some performance issues related with the metadata loading, which sometimes
>>>>> blocks the GUI, as you are describing. Is this happening to  you when many
>>>>> protocols are in ‘running’ state? Or just when the project has many
>>>>> protocols? We are working to find a solution to this problem and make the
>>>>> processing with Scipion more effective, sorry for the inconveniences.
>>>>>
>>>>> All the best,
>>>>> Pablo
>>>>> Scipion team.
>>>>>
>>>>>
>>>>>
>>>>> On 26/09/16 15:52, Сергей Назаров wrote:
>>>>>
>>>>>> Dear Scipion Community,
>>>>>>
>>>>>> I constantly experience issue with loading metadata to my projects.
>>>>>> It can get really annoying, I wait sometimes almost a minute to be
>>>>>> able to adjust the description of a protocol, choose data (particles.
>>>>>> models etc.). I found this behavior both on local machines and on cluster
>>>>>> through ssh. While I can understand slow metadata loading through ssh,
>>>>>> especially for a big project with many protocols already executed, on local
>>>>>> machine this behavior appears after sometime after reboot. I don't know if
>>>>>> it starts after some threshold amount of protocols or not, but after
>>>>>> machine reboot everything runs nice and smooth for certain time and then
>>>>>> starts again.
>>>>>> I found one closed request on github concerning slow metadata, but
>>>>>> without any details.
>>>>>> Could you please advise me something about this issue? How to behave
>>>>>> when your project is on cluster and metadata is slow? I am not superuser,
>>>>>> so I am not able to reboot nodes everytime.
>>>>>>
>>>>>> Best,
>>>>>> Sergey Nazarov
>>>>>> Biozentrum Basel
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>>
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>>>
>>>
>>
>

Re: [scipion-users] Metadata loading

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

Thanks Sergey,

I think that you should split that into different projects if it is really
another project. If it is the same one, it make sense to add to the current
one. But this would be a way to alleviate the current issue. We will let
you know about any progress related this. Thanks a lot for sharing the
project.sqlite database for further inspection.

Cheers,
Jose Miguel.



On Thu, Sep 29, 2016 at 10:17 AM, Сергей Назаров <ser...@un...>
wrote:

> Dear Jose, Pablo,
>
> Here is the project file, I also attach settings file just in case.
> Yes, the tree is really big, I simply add branches as soon is new data is
> arriving. So, for future I would try to split the data into as many
> projects as possible.
>
> Best,
> Sergey
>
> 2016-09-28 11:23 GMT+02:00 Jose Miguel de la Rosa Trevin <
> del...@gm...>:
>
>> Dear Serguey,
>>
>> As Pablo said, thanks for given us important feedback. Could you share
>> you project.sqlite databaset with us? So we can perform some tests on it.
>> It should work with this number of runs and this would be smother after we
>> fix some refresh problems.
>>
>> Kind regards,
>> Jose Miguel.
>>
>>
>> On Wed, Sep 28, 2016 at 11:00 AM, Pablo <p.c...@gm...> wrote:
>>
>>> Wow! We certainly need to have your case in mind (589 runs) when testing
>>> performance.
>>> Collapsing some branches actually reduce "drawing time" but the whole
>>> project is loaded which takes most of the time.
>>>
>>> Now I can't see any other workaround than deleting runs. If you want to
>>> keep them all, another option could be to copy the project folder (watch
>>> out for the disk space), and in the new project delete runs.
>>> But I can understand this way you loose the whole picture of the project.
>>>
>>> I've added your case into our issue, and will discuss your case in our
>>> next development meeting.
>>>
>>> :-(
>>>
>>> Pablo.
>>>
>>>
>>> On 27/09/16 16:26, Сергей Назаров wrote:
>>>
>>> Dear Pablo,
>>>
>>> Thank you for a quick reply. Unfortunately, I don't have many protocols
>>> running at the same time, usually from 1 to 3. But the project is huge, the
>>> number of folders in Runs/ is 589. I keep most of branches collapsed,
>>> hopefully it prevent them from loading.
>>>
>>> Best,
>>> Sergey
>>>
>>> 2016-09-26 19:00 GMT+02:00 Pablo <p.c...@gm...>:
>>>
>>>> Dear Sergey,
>>>>
>>>> Thanks a lot for your feedback, this is very important for us to know
>>>> important issues and also to give priority to new features. We are aware of
>>>> some performance issues related with the metadata loading, which sometimes
>>>> blocks the GUI, as you are describing. Is this happening to  you when many
>>>> protocols are in ‘running’ state? Or just when the project has many
>>>> protocols? We are working to find a solution to this problem and make the
>>>> processing with Scipion more effective, sorry for the inconveniences.
>>>>
>>>> All the best,
>>>> Pablo
>>>> Scipion team.
>>>>
>>>>
>>>>
>>>> On 26/09/16 15:52, Сергей Назаров wrote:
>>>>
>>>>> Dear Scipion Community,
>>>>>
>>>>> I constantly experience issue with loading metadata to my projects.
>>>>> It can get really annoying, I wait sometimes almost a minute to be
>>>>> able to adjust the description of a protocol, choose data (particles.
>>>>> models etc.). I found this behavior both on local machines and on cluster
>>>>> through ssh. While I can understand slow metadata loading through ssh,
>>>>> especially for a big project with many protocols already executed, on local
>>>>> machine this behavior appears after sometime after reboot. I don't know if
>>>>> it starts after some threshold amount of protocols or not, but after
>>>>> machine reboot everything runs nice and smooth for certain time and then
>>>>> starts again.
>>>>> I found one closed request on github concerning slow metadata, but
>>>>> without any details.
>>>>> Could you please advise me something about this issue? How to behave
>>>>> when your project is on cluster and metadata is slow? I am not superuser,
>>>>> so I am not able to reboot nodes everytime.
>>>>>
>>>>> Best,
>>>>> Sergey Nazarov
>>>>> Biozentrum Basel
>>>>>
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>
>

Re: [scipion-users] Metadata loading

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

Dear Serguey,

As Pablo said, thanks for given us important feedback. Could you share you
project.sqlite databaset with us? So we can perform some tests on it. It
should work with this number of runs and this would be smother after we fix
some refresh problems.

Kind regards,
Jose Miguel.


On Wed, Sep 28, 2016 at 11:00 AM, Pablo <p.c...@gm...> wrote:

> Wow! We certainly need to have your case in mind (589 runs) when testing
> performance.
> Collapsing some branches actually reduce "drawing time" but the whole
> project is loaded which takes most of the time.
>
> Now I can't see any other workaround than deleting runs. If you want to
> keep them all, another option could be to copy the project folder (watch
> out for the disk space), and in the new project delete runs.
> But I can understand this way you loose the whole picture of the project.
>
> I've added your case into our issue, and will discuss your case in our
> next development meeting.
>
> :-(
>
> Pablo.
>
>
> On 27/09/16 16:26, Сергей Назаров wrote:
>
> Dear Pablo,
>
> Thank you for a quick reply. Unfortunately, I don't have many protocols
> running at the same time, usually from 1 to 3. But the project is huge, the
> number of folders in Runs/ is 589. I keep most of branches collapsed,
> hopefully it prevent them from loading.
>
> Best,
> Sergey
>
> 2016-09-26 19:00 GMT+02:00 Pablo <p.c...@gm...>:
>
>> Dear Sergey,
>>
>> Thanks a lot for your feedback, this is very important for us to know
>> important issues and also to give priority to new features. We are aware of
>> some performance issues related with the metadata loading, which sometimes
>> blocks the GUI, as you are describing. Is this happening to  you when many
>> protocols are in ‘running’ state? Or just when the project has many
>> protocols? We are working to find a solution to this problem and make the
>> processing with Scipion more effective, sorry for the inconveniences.
>>
>> All the best,
>> Pablo
>> Scipion team.
>>
>>
>>
>> On 26/09/16 15:52, Сергей Назаров wrote:
>>
>>> Dear Scipion Community,
>>>
>>> I constantly experience issue with loading metadata to my projects.
>>> It can get really annoying, I wait sometimes almost a minute to be able
>>> to adjust the description of a protocol, choose data (particles. models
>>> etc.). I found this behavior both on local machines and on cluster through
>>> ssh. While I can understand slow metadata loading through ssh, especially
>>> for a big project with many protocols already executed, on local machine
>>> this behavior appears after sometime after reboot. I don't know if it
>>> starts after some threshold amount of protocols or not, but after machine
>>> reboot everything runs nice and smooth for certain time and then starts
>>> again.
>>> I found one closed request on github concerning slow metadata, but
>>> without any details.
>>> Could you please advise me something about this issue? How to behave
>>> when your project is on cluster and metadata is slow? I am not superuser,
>>> so I am not able to reboot nodes everytime.
>>>
>>> Best,
>>> Sergey Nazarov
>>> Biozentrum Basel
>>>
>>
>>
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] Metadata loading

[Pablo <p.c...@gm...>]

Wow! We certainly need to have your case in mind (589 runs) when testing 
performance.

Collapsing some branches actually reduce "drawing time" but the whole 
project is loaded which takes most of the time.

Now I can't see any other workaround than deleting runs. If you want to 
keep them all, another option could be to copy the project folder (watch 
out for the disk space), and in the new project delete runs.
But I can understand this way you loose the whole picture of the project.

I've added your case into our issue, and will discuss your case in our 
next development meeting.

:-(

Pablo.

On 27/09/16 16:26, Сергей Назаров wrote:
> Dear Pablo,
>
> Thank you for a quick reply. Unfortunately, I don't have many 
> protocols running at the same time, usually from 1 to 3. But the 
> project is huge, the number of folders in Runs/ is 589. I keep most of 
> branches collapsed, hopefully it prevent them from loading.
>
> Best,
> Sergey
>
> 2016-09-26 19:00 GMT+02:00 Pablo <p.c...@gm... 
> <mailto:p.c...@gm...>>:
>
>     Dear Sergey,
>
>     Thanks a lot for your feedback, this is very important for us to
>     know important issues and also to give priority to new features.
>     We are aware of some performance issues related with the metadata
>     loading, which sometimes blocks the GUI, as you are describing. Is
>     this happening to  you when many protocols are in ‘running’ state?
>     Or just when the project has many protocols? We are working to
>     find a solution to this problem and make the processing with
>     Scipion more effective, sorry for the inconveniences.
>
>     All the best,
>     Pablo
>     Scipion team.
>
>
>
>     On 26/09/16 15:52, Сергей Назаров wrote:
>
>         Dear Scipion Community,
>
>         I constantly experience issue with loading metadata to my
>         projects.
>         It can get really annoying, I wait sometimes almost a minute
>         to be able to adjust the description of a protocol, choose
>         data (particles. models etc.). I found this behavior both on
>         local machines and on cluster through ssh. While I can
>         understand slow metadata loading through ssh, especially for a
>         big project with many protocols already executed, on local
>         machine this behavior appears after sometime after reboot. I
>         don't know if it starts after some threshold amount of
>         protocols or not, but after machine reboot everything runs
>         nice and smooth for certain time and then starts again.
>         I found one closed request on github concerning slow metadata,
>         but without any details.
>         Could you please advise me something about this issue? How to
>         behave when your project is on cluster and metadata is slow? I
>         am not superuser, so I am not able to reboot nodes everytime.
>
>         Best,
>         Sergey Nazarov
>         Biozentrum Basel
>
>
>

Re: [scipion-users] Metadata loading

[Сергей Н. <ser...@un...>]

Dear Pablo,

Thank you for a quick reply. Unfortunately, I don't have many protocols
running at the same time, usually from 1 to 3. But the project is huge, the
number of folders in Runs/ is 589. I keep most of branches collapsed,
hopefully it prevent them from loading.

Best,
Sergey

2016-09-26 19:00 GMT+02:00 Pablo <p.c...@gm...>:

> Dear Sergey,
>
> Thanks a lot for your feedback, this is very important for us to know
> important issues and also to give priority to new features. We are aware of
> some performance issues related with the metadata loading, which sometimes
> blocks the GUI, as you are describing. Is this happening to  you when many
> protocols are in ‘running’ state? Or just when the project has many
> protocols? We are working to find a solution to this problem and make the
> processing with Scipion more effective, sorry for the inconveniences.
>
> All the best,
> Pablo
> Scipion team.
>
>
>
> On 26/09/16 15:52, Сергей Назаров wrote:
>
>> Dear Scipion Community,
>>
>> I constantly experience issue with loading metadata to my projects.
>> It can get really annoying, I wait sometimes almost a minute to be able
>> to adjust the description of a protocol, choose data (particles. models
>> etc.). I found this behavior both on local machines and on cluster through
>> ssh. While I can understand slow metadata loading through ssh, especially
>> for a big project with many protocols already executed, on local machine
>> this behavior appears after sometime after reboot. I don't know if it
>> starts after some threshold amount of protocols or not, but after machine
>> reboot everything runs nice and smooth for certain time and then starts
>> again.
>> I found one closed request on github concerning slow metadata, but
>> without any details.
>> Could you please advise me something about this issue? How to behave when
>> your project is on cluster and metadata is slow? I am not superuser, so I
>> am not able to reboot nodes everytime.
>>
>> Best,
>> Sergey Nazarov
>> Biozentrum Basel
>>
>
>

Re: [scipion-users] Metadata loading

[Pablo <p.c...@gm...>]

Dear Sergey,

Thanks a lot for your feedback, this is very important for us to know 
important issues and also to give priority to new features. We are aware 
of some performance issues related with the metadata loading, which 
sometimes blocks the GUI, as you are describing. Is this happening to  
you when many protocols are in ‘running’ state? Or just when the project 
has many protocols? We are working to find a solution to this problem 
and make the processing with Scipion more effective, sorry for the 
inconveniences.

All the best,
Pablo
Scipion team.


On 26/09/16 15:52, Сергей Назаров wrote:
> Dear Scipion Community,
>
> I constantly experience issue with loading metadata to my projects.
> It can get really annoying, I wait sometimes almost a minute to be 
> able to adjust the description of a protocol, choose data (particles. 
> models etc.). I found this behavior both on local machines and on 
> cluster through ssh. While I can understand slow metadata loading 
> through ssh, especially for a big project with many protocols already 
> executed, on local machine this behavior appears after sometime after 
> reboot. I don't know if it starts after some threshold amount of 
> protocols or not, but after machine reboot everything runs nice and 
> smooth for certain time and then starts again.
> I found one closed request on github concerning slow metadata, but 
> without any details.
> Could you please advise me something about this issue? How to behave 
> when your project is on cluster and metadata is slow? I am not 
> superuser, so I am not able to reboot nodes everytime.
>
> Best,
> Sergey Nazarov
> Biozentrum Basel

[scipion-users] Metadata loading

[Сергей Н. <ser...@un...>]

Dear Scipion Community,

I constantly experience issue with loading metadata to my projects.
It can get really annoying, I wait sometimes almost a minute to be able to
adjust the description of a protocol, choose data (particles. models etc.).
I found this behavior both on local machines and on cluster through ssh.
While I can understand slow metadata loading through ssh, especially for a
big project with many protocols already executed, on local machine this
behavior appears after sometime after reboot. I don't know if it starts
after some threshold amount of protocols or not, but after machine reboot
everything runs nice and smooth for certain time and then starts again.
I found one closed request on github concerning slow metadata, but without
any details.
Could you please advise me something about this issue? How to behave when
your project is on cluster and metadata is slow? I am not superuser, so I
am not able to reboot nodes everytime.

Best,
Sergey Nazarov
Biozentrum Basel

Re: [scipion-users] Downsampling/binning

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

Dear Dmitry,

you have 2 options depending in which step you are in.


1.- If you are extracting the particles, you can choose "other" in 
"Micrographs source", and then specify a "Downsampling factor"



2.- or..if you have already extracted the particles or imported them 
from somewhere else you can use

the "crop/resize particles" protocol. The easiest way to find any 
protocol is to:

a.- type "Control + F": a search dialog should pop up.

b.- Type, for this case, "crop" in the text box and enter.

c.- Choose, in this case the "xmipp3 - crop/resize particles"


I hope this help. Please send another email if you need more help.

All the best, Pablo.


On 16/09/16 16:55, Dmitry A. Semchonok wrote:
> Dear colleagues,
>
> Is there a tool to downsample the extracted particles?
>
> Sincerely,
> Dmitry
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[scipion-users] Downsampling/binning

[Dmitry A. S. <sem...@gm...>]

Dear colleagues,

Is there a tool to downsample the extracted particles?

Sincerely,
Dmitry

Re: [scipion-users] xmipp3- ctf--> NonAstigmaticValidity-->2d classification ctf correction

[Carlos O. S. <co...@cn...>]

Dear Dmitry,

in principle correcting for the astigmatism while reconstructing could 
be possible. In practice, the angle of the defoci in the micrograph 
should be taken into account for this correction and no 3D 
reconstruction program is currently considering it, so it is better to 
keep low the astigmatism.

The main parameters to determine the quality of the micrographs are:

- ctfCritMaxFreq: in Angstroms which is the maximum resolution expected 
due to envelope

- ctfCritNonAstigmaticValidity: in Angstroms which is the maximum 
resolution due to astigmatism

- ctfCritCtfMargin and ctfCritCorr13: the higher, the better. It is 
related to how visible Thon rings are

- ctfCritPSDCorr90: it can detect drift and astigmatism, should be very 
close to 1 for good micrographs

- ctfCritFirstZeroRatio: it can detect astigmatism. It should be very 
close to 1 for good micrographs

Kind regards, Carlos Oscar


On 15/09/2016 15:53, Dmitry A. Semchonok wrote:
> Dear colleagues,
>
> My question is about xmipp3- ctf estimation.
>
> In that protocol we have the NonAstigmaticValidity parameter.
> I would like to ask if knowing this parameter later the protocol relion 2d
> (3d)classification is correcting for that astigmatism or it is better to
> remove the images where this NonAstigmaticValidity is quite high (higher
> the resolution you expect)?
>
> Which parameter in xmipp3-ctf by your experience is the most crucial and
> requires to kick the bad images out?
>
> Sincerely,
> Dmitry
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

-- 
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
------------------------------------------------------------------------

[scipion-users] xmipp3- ctf--> NonAstigmaticValidity-->2d classification ctf correction

[Dmitry A. S. <sem...@gm...>]

Dear colleagues,

My question is about xmipp3- ctf estimation.

In that protocol we have the NonAstigmaticValidity parameter.
I would like to ask if knowing this parameter later the protocol relion 2d  
(3d)classification is correcting for that astigmatism or it is better to 
remove the images where this NonAstigmaticValidity is quite high (higher 
the resolution you expect)?

Which parameter in xmipp3-ctf by your experience is the most crucial and 
requires to kick the bad images out?

Sincerely,
Dmitry

Re: [scipion-users] Error in xmipp particle picking

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

Dear Ashutosh,

Thanks for re-sending your mail to this list. We will try to reproduce your
problem and let you know.

Bests,
Jose Miguel.


On Thu, Sep 15, 2016 at 2:00 PM, ashutosh srivastava <ash...@gm...>
wrote:

> Dear Scipion and xmipp users
>
> I posted the following in newxmipp users list which I have now learnt is
> no longer active, so this is a repost. Sorry if this gets repeated in your
> inbox.
>
>
> I am trying to pick particles from imported micrographs in Scipion GUI,
> but keep getting this error
> "No enum constant xmipp.viewer.particlepicker.training.model.Mode"
> Following are some relevant details.
> Micrographs imported from tif files and import finished without any
> errors, I can see the micrographs with in scipion.
> The xmipp3-manual-picking (step1) application dialogue box opens and I can
> enter the micrograph location, however upon execution the above mentioned
> error pops up. Following gets echoed on terminal
>
> *java.lang.IllegalArgumentException: No enum constant
> xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.Mode.*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.loadConfig(SupervisedParticlePicker.java:638)*
> * at xmipp.viewer.particlepicker.Pa
> <http://xmipp.viewer.particlepicker.Pa>rticlePicker.<init>(ParticlePicker.java:149)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:79)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:72)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:125)*
> * at xmipp.viewer.particlepicker.tr
> <http://xmipp.viewer.particlepicker.tr>aining.SupervisedPickerRunner.run(SupervisedPickerRunner.java:33)*
> * at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)*
> * at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)*
> * at java.awt.EventQueue.access$500(EventQueue.java:97)*
> * at java.awt.EventQueue$3.run(EventQueue.java:709)*
> * at java.awt.EventQueue$3.run(EventQueue.java:703)*
> * at java.security.AccessController.doPrivileged(Native Method)*
> * at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)*
> * at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)*
> * at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)*
> * at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)*
> * at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)*
> * at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)*
>
> In the terminal following warnings keep repeating
>
> *WARNING: MetaData: Error parsing column 'particleSize' value.*
> *WARNING: MetaData: Error parsing column 'autopickPercent' value.*
> *WARNING: MetaData: Error parsing column 'templatesNum' value.*
> *WARNING: MetaData: Error parsing column 'pickingState' value.*
> *WARNING: MetaData: Error parsing column 'manualParticlesNum' value.*
> *WARNING: MetaData: Error parsing column 'autoParticlesNum' value.*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
>
> I am using scipion v1.0.0 and in the current project I just imported the
> micrographs and then particle picking.
> I can still open the interactive manual picking run in earlier projects as
> well as I can start a new manual picking run in older already saved
> projects (in which the picking has already been done). It seems the problem
> occurs when I am trying to start a new particle picking run in a new
> project.
> The general config file looks like following, where /path/to/mpi is my
> path to mpi. However, since earlier projects are running fine I think its
> unlikely that the problem lies here.
>
> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion
> SCIPION_URL_TESTDATA = %(SCIPION_URL)s/data/tests
> SCIPION_URL_SOFTWARE = %(SCIPION_URL)s/software
>
> [DIRS_GLOBAL]
> SCIPION_SOFTWARE = software
> SCIPION_TESTS = data/tests
>
> [BUILD]
> LINKERFORPROGRAMS = g++
> CXXFLAGS =
> GTEST = False
> MPI_LINKERFORPROGRAMS = mpiCC
> MPI_LIB = openmpi
> MPI_BINDIR = path/to/mpi/bin
> JNI_CPPPATH = %(JAVA_HOME)s/include:%(JAVA_HOME)s/include/linux
> OPENCV = True
> MPI_CC = mpicc
> CUDA = False
> JAVA_HOME = /usr/lib/jvm/java-1.8.0-openjdk
> MATLAB = False
> JAVA_BINDIR = %(JAVA_HOME)s/bin
> CC = gcc
> JAR = %(JAVA_BINDIR)s/jar
> MPI_CXX = mpiCC
> DEBUG = False
> MPI_LIBDIR = /path/to/mpi/lib
> JAVAC = %(JAVA_BINDIR)s/javac
> CXX = g++
> LINKFLAGS =
> CCFLAGS = -std=c99
> MATLAB_DIR = /usr/local/MATLAB/R2011a
> MPI_INCLUDE = /path/to/mpi/include
>
> Thank you. Kindly let me know if any more details are required.
>
> Best Regards
> Ashutosh
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] Error in xmipp particle picking

[ashutosh s. <ash...@gm...>]

Dear Scipion and xmipp users

I posted the following in newxmipp users list which I have now learnt is no
longer active, so this is a repost. Sorry if this gets repeated in your
inbox.


I am trying to pick particles from imported micrographs in Scipion GUI, but
keep getting this error
"No enum constant xmipp.viewer.particlepicker.training.model.Mode"
Following are some relevant details.
Micrographs imported from tif files and import finished without any errors,
I can see the micrographs with in scipion.
The xmipp3-manual-picking (step1) application dialogue box opens and I can
enter the micrograph location, however upon execution the above mentioned
error pops up. Following gets echoed on terminal

*java.lang.IllegalArgumentException: No enum constant
xmipp.viewer.particlepicker.training.model.Mode.*
* at
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadConfig(SupervisedParticlePicker.java:638)*
* at
xmipp.viewer.particlepicker.ParticlePicker.<init>(ParticlePicker.java:149)*
* at
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:79)*
* at
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:72)*
* at
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:125)*
* at
xmipp.viewer.particlepicker.training.SupervisedPickerRunner.run(SupervisedPickerRunner.java:33)*
* at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)*
* at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)*
* at java.awt.EventQueue.access$500(EventQueue.java:97)*
* at java.awt.EventQueue$3.run(EventQueue.java:709)*
* at java.awt.EventQueue$3.run(EventQueue.java:703)*
* at java.security.AccessController.doPrivileged(Native Method)*
* at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)*
* at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)*
* at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)*
* at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)*
* at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)*
* at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)*
* at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)*
* at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)*

In the terminal following warnings keep repeating

*WARNING: MetaData: Error parsing column 'particleSize' value.*
*WARNING: MetaData: Error parsing column 'autopickPercent' value.*
*WARNING: MetaData: Error parsing column 'templatesNum' value.*
*WARNING: MetaData: Error parsing column 'pickingState' value.*
*WARNING: MetaData: Error parsing column 'manualParticlesNum' value.*
*WARNING: MetaData: Error parsing column 'autoParticlesNum' value.*
*WARNING!!! valueIn.failed = True, binding NULL*
*WARNING!!! valueIn.failed = True, binding NULL*
*WARNING!!! valueIn.failed = True, binding NULL*
*WARNING!!! valueIn.failed = True, binding NULL*
*WARNING!!! valueIn.failed = True, binding NULL*
*WARNING!!! valueIn.failed = True, binding NULL*

I am using scipion v1.0.0 and in the current project I just imported the
micrographs and then particle picking.
I can still open the interactive manual picking run in earlier projects as
well as I can start a new manual picking run in older already saved
projects (in which the picking has already been done). It seems the problem
occurs when I am trying to start a new particle picking run in a new
project.
The general config file looks like following, where /path/to/mpi is my path
to mpi. However, since earlier projects are running fine I think its
unlikely that the problem lies here.

SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion
SCIPION_URL_TESTDATA = %(SCIPION_URL)s/data/tests
SCIPION_URL_SOFTWARE = %(SCIPION_URL)s/software

[DIRS_GLOBAL]
SCIPION_SOFTWARE = software
SCIPION_TESTS = data/tests

[BUILD]
LINKERFORPROGRAMS = g++
CXXFLAGS =
GTEST = False
MPI_LINKERFORPROGRAMS = mpiCC
MPI_LIB = openmpi
MPI_BINDIR = path/to/mpi/bin
JNI_CPPPATH = %(JAVA_HOME)s/include:%(JAVA_HOME)s/include/linux
OPENCV = True
MPI_CC = mpicc
CUDA = False
JAVA_HOME = /usr/lib/jvm/java-1.8.0-openjdk
MATLAB = False
JAVA_BINDIR = %(JAVA_HOME)s/bin
CC = gcc
JAR = %(JAVA_BINDIR)s/jar
MPI_CXX = mpiCC
DEBUG = False
MPI_LIBDIR = /path/to/mpi/lib
JAVAC = %(JAVA_BINDIR)s/javac
CXX = g++
LINKFLAGS =
CCFLAGS = -std=c99
MATLAB_DIR = /usr/local/MATLAB/R2011a
MPI_INCLUDE = /path/to/mpi/include

Thank you. Kindly let me know if any more details are required.

Best Regards
Ashutosh

[scipion-users] Scipion September newsletter....

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

Again, sorry to disturb you, but we want to share our progress with you, 
here is  this month's newsletter.


      September 2016


        <https://github.com/I2PC/scipion/wiki/Newsletters#published-results-using-scipion>Published
        results using Scipion

We are glad to see the first three publications using Scipion!

  *

    The Yaser Hasem group
    <http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique151&lang=en>in
    Strasbourg reported the structure of a mammalian 48S initiation
    complex at 5.8 Å resolution, showing the relocation of subunits
    eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding
    site, at the late stage in initiation.

  *

    In collaboration withRoman Koning in Leiden
    <https://www.lumc.nl/org/moleculaire-celbiologie/medewerkers/RomanKoning?setlanguage=English&setcountry=en>,
    the asymmetric virion structure of bacteriophage MS2 was determined
    and it was found that, in situ, the viral RNA genome can form a
    branched network of stem-loops that almost all allocate near the
    capsid inner surface, while predominantly binding to coat protein
    dimers that are located in one-half of the capsid.

  *

    Also from Roman Koning group theStructure of AP205 (single RNA
    stranded phage) Coat Protein
    <http://dx.doi.org/10.1016/j.jmb.2016.08.025>is been reconstructed
    to 6.0-Å.


        <https://github.com/I2PC/scipion/wiki/Newsletters#new-protocols-integrated>New
        protocols integrated

  *

    At the end of July, we received the visit of Hans Elmlund, the main
    developer ofSimple <http://simplecryoem.com/>. We have created a set
    of protocols for most of the Simple2.0 programs. We are doing more
    testing and plan to release them in the next Scipion version.

  *

    Two new protocols were added: MotionCor2 for movie processing on
    multi-GPU (from D. Agard lab), estimation/correction of
    magnification distortion (from N. Grigorieff’s lab). They are
    available in devel version of Scipion. See the detailshere
    <https://github.com/I2PC/scipion/wiki/Integrated-Packages>


You can see this online here 
<https://github.com/I2PC/scipion/wiki/Newsletters#september-2016>


All the best, Pablo

Scipion development team.

Re: [scipion-users] Exporting coordinates from 1 pc to the 2 pc

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

Dear Dmitry,

All pos files are under the 'extra' folder of your picking folder. For
example, in my project:

TutorialBetagal_FromBox/Runs/000192_XmippProtParticlePicking/extra

You can copy the extra folder to pc 2...and open a new Xmipp picking job
on the project there...and you can import all the .pos files at once.
Go to File -> Import Coordinates and select the folder where you have
copied the .pos files. You can visually inspect if the import was
sucessfully
for each micrograph.

Hope this helps,
Bests,
Jose Miguel


On Thu, Sep 15, 2016 at 10:49 AM, Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> For some reason I pick the particles on 1 pc and process them on the
> another - using xmipp manual / auto picking protocol.
>
> Could you tell me how can i export all picked position from 1 pc to the 2
> pc?
>
> P.s. I tried to save the positions as *.pos file on pc 1 but then when I
> want to apply this *. pos file to 2 pc I get export only 1 by 1 image and
> not all together.
>
> Sincerely,
> Dmitry
>
>
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Exporting coordinates from 1 pc to the 2 pc

[Dmitry A. S. <sem...@gm...>]

Dear colleagues,

For some reason I pick the particles on 1 pc and process them on the 
another - using xmipp manual / auto picking protocol.

Could you tell me how can i export all picked position from 1 pc to the 2 pc?

P.s. I tried to save the positions as *.pos file on pc 1 but then when I 
want to apply this *. pos file to 2 pc I get export only 1 by 1 image and 
not all together.

Sincerely,
Dmitry

Re: [scipion-users] [Xmipp-users] Error in xmipp particle picking

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

Dear Ashutosh,

As Grigory already pointed out, we are moving from newxmipp-users to the
more general scipion-users mailing list.
Sorry for the late response. Could you provide more details about the
problem? (as Grigory said, the Scipion version)
You have only imported the Micrographs and then Particle picking?

Bests,
Jose Miguel.


On Mon, Sep 12, 2016 at 3:47 PM, Grigory Sharov <sha...@gm...>
wrote:

> Hello Ashutosh,
>
> my guess is newxmipp-users list is kind of "dead", so it is better to
> write to *sci...@li...
> <sci...@li...>*
>
> What is scipion version you are using? I.e., which git branch you are on:
> master or v1.0, devel?
>
> Best regards,
> Grigory
>
> ------------------------------------------------------------
> --------------------
> Grigory Sharov, Ph.D.
> Institute of Genetics and Molecular and Cellular Biology
> Integrated Structural Biology Department (CBI)
> 1, rue Laurent Fries
> 67404 Illkirch, France
> tel. 03 69 48 51 00
> e-mail: sh...@ig...
>
> On Thu, Sep 8, 2016 at 6:08 AM, ashutosh srivastava <ash...@gm...>
> wrote:
>
>> Dear Scipion and xmipp users
>>
>> I am trying to pick particles from imported micrographs in Scipion GUI,
>> but keep getting this error
>> "No enum constant xmipp.viewer.particlepicker.training.model.Mode"
>> Following are some relevant details.
>> Micrographs imported from tif files and import finished without any
>> errors, I can see the micrographs with in scipion.
>> The xmipp3-manual-picking (step1) application dialogue box opens and I
>> can enter the micrograph location, however upon execution the above
>> mentioned error pops up. Following gets echoed on terminal
>>
>> *java.lang.IllegalArgumentException: No enum constant
>> xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.model.Mode.*
>> * at xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.loadConfig(SupervisedParticlePicker.java:638)*
>> * at xmipp.viewer.particlepicker.Pa
>> <http://xmipp.viewer.particlepicker.Pa>rticlePicker.<init>(ParticlePicker.java:149)*
>> * at xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:79)*
>> * at xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:72)*
>> * at xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:125)*
>> * at xmipp.viewer.particlepicker.tr
>> <http://xmipp.viewer.particlepicker.tr>aining.SupervisedPickerRunner.run(SupervisedPickerRunner.java:33)*
>> * at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)*
>> * at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)*
>> * at java.awt.EventQueue.access$500(EventQueue.java:97)*
>> * at java.awt.EventQueue$3.run(EventQueue.java:709)*
>> * at java.awt.EventQueue$3.run(EventQueue.java:703)*
>> * at java.security.AccessController.doPrivileged(Native Method)*
>> * at
>> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)*
>> * at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)*
>> * at
>> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)*
>> * at
>> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)*
>> * at
>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)*
>> * at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)*
>> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)*
>> * at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)*
>>
>> In the terminal following warnings keep repeating
>>
>> *WARNING: MetaData: Error parsing column 'particleSize' value.*
>> *WARNING: MetaData: Error parsing column 'autopickPercent' value.*
>> *WARNING: MetaData: Error parsing column 'templatesNum' value.*
>> *WARNING: MetaData: Error parsing column 'pickingState' value.*
>> *WARNING: MetaData: Error parsing column 'manualParticlesNum' value.*
>> *WARNING: MetaData: Error parsing column 'autoParticlesNum' value.*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>> *WARNING!!! valueIn.failed = True, binding NULL*
>>
>> Kindly let me know if any other details are required.
>>
>> Thank you
>>
>> Best Regards
>> Ashutosh
>>
>>
>> ------------------------------------------------------------
>> ------------------
>>
>> _______________________________________________
>> Newxmipp-users mailing list
>> New...@li...
>> https://lists.sourceforge.net/lists/listinfo/newxmipp-users
>>
>>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] [Xmipp-users] Error in xmipp particle picking

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

Hello Ashutosh,

my guess is newxmipp-users list is kind of "dead", so it is better to write
to *sci...@li...
<sci...@li...>*

What is scipion version you are using? I.e., which git branch you are on:
master or v1.0, devel?

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
Institute of Genetics and Molecular and Cellular Biology
Integrated Structural Biology Department (CBI)
1, rue Laurent Fries
67404 Illkirch, France
tel. 03 69 48 51 00
e-mail: sh...@ig...

On Thu, Sep 8, 2016 at 6:08 AM, ashutosh srivastava <ash...@gm...>
wrote:

> Dear Scipion and xmipp users
>
> I am trying to pick particles from imported micrographs in Scipion GUI,
> but keep getting this error
> "No enum constant xmipp.viewer.particlepicker.training.model.Mode"
> Following are some relevant details.
> Micrographs imported from tif files and import finished without any
> errors, I can see the micrographs with in scipion.
> The xmipp3-manual-picking (step1) application dialogue box opens and I can
> enter the micrograph location, however upon execution the above mentioned
> error pops up. Following gets echoed on terminal
>
> *java.lang.IllegalArgumentException: No enum constant
> xmipp.viewer.particlepicker.training.model.Mode.*
> * at
> xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadConfig(SupervisedParticlePicker.java:638)*
> * at
> xmipp.viewer.particlepicker.ParticlePicker.<init>(ParticlePicker.java:149)*
> * at
> xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:79)*
> * at
> xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:72)*
> * at
> xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.<init>(SupervisedParticlePicker.java:125)*
> * at
> xmipp.viewer.particlepicker.training.SupervisedPickerRunner.run(SupervisedPickerRunner.java:33)*
> * at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)*
> * at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)*
> * at java.awt.EventQueue.access$500(EventQueue.java:97)*
> * at java.awt.EventQueue$3.run(EventQueue.java:709)*
> * at java.awt.EventQueue$3.run(EventQueue.java:703)*
> * at java.security.AccessController.doPrivileged(Native Method)*
> * at
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)*
> * at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)*
> * at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)*
> * at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)*
> * at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)*
> * at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)*
> * at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)*
>
> In the terminal following warnings keep repeating
>
> *WARNING: MetaData: Error parsing column 'particleSize' value.*
> *WARNING: MetaData: Error parsing column 'autopickPercent' value.*
> *WARNING: MetaData: Error parsing column 'templatesNum' value.*
> *WARNING: MetaData: Error parsing column 'pickingState' value.*
> *WARNING: MetaData: Error parsing column 'manualParticlesNum' value.*
> *WARNING: MetaData: Error parsing column 'autoParticlesNum' value.*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
> *WARNING!!! valueIn.failed = True, binding NULL*
>
> Kindly let me know if any other details are required.
>
> Thank you
>
> Best Regards
> Ashutosh
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> Newxmipp-users mailing list
> New...@li...
> https://lists.sourceforge.net/lists/listinfo/newxmipp-users
>
>

Re: [scipion-users] movie alignment

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

Dear Dmitry,

Defining which is "the best" is nearly impossible in most contexts. As you
may know, some algorithms perform better than other for some cases, but not
for all situations.
Following are some comments from our experience here in our lab, other may
have a totally different opinion.

We have extensively tested MotionCor and Optical Flow, which are both
integrated into Scipion. Optical Flow is quite a sophisticated approach to
handle local movements, and it was a joint work with Li and Yifan. .. More
about it at:

Alignment of direct detection device micrographs using a robust Optical
Flow approach. <http://www.ncbi.nlm.nih.gov/pubmed/25681631>
Abrishami V, Vargas J, Li X, Cheng Y, Marabini R, Sorzano CÓ, Carazo JM.
J Struct Biol. 2015 Mar;189(3):163-76.


Further along this line, during this year we have processed most of the Map
Challenge data sets with both methods, and the empirical conclusion that we
are reaching so far is that:


-For Falcon data: The combination of MotionCor and Optical Flow always
gives better results than MotionCor alone

-For K2 data: MotionCor works very well and Optical Flow just does very
little improvement.


Note that MotionCorr2 is already integrated into Scipion(in devel branch,
thanks to Grigory Sharov), but we have not extensively tested yet.


Hope this helps,

Jose Miguel.




On Sat, Sep 10, 2016 at 10:58 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> What protocol by your experience is the best for the alignment of movies
> (if you use K2)?
>
> Sincerely,
>
> Dmitry
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] movie alignment

[Dmitry S. <sem...@gm...>]

Dear colleagues,

What protocol by your experience is the best for the alignment of movies
(if you use K2)?

Sincerely,

Dmitry

Re: [scipion-users] reference based particle picking

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

Dear Dmitry,

For doing what you want, there are 3 steps:

1) Create a set of projection in the command line.
Use 'scipion xmipp_angular_project_library', this Xmipp program mainly
requires the input Volume, the output stack and the distance in degrees
between projections.
Additionally, you can provide symmetry if known. (We could easily add a
protocol wrapping in the future)

2) Import the generated projections in 1) as SetOfAverages (protocol -
import averages)

3) Select any picking that use references (e.g., Relion autopicking(two
steps), IGBMC GemPicker or Gautomatch)

Hope this helps
Jose Miguel.


On Wed, Sep 7, 2016 at 11:42 AM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> Could you please tell me how to create a (multi)reference for the particle
> picking?
>
> (I have 3d model of the required particle)
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] reference based particle picking

[Dmitry S. <sem...@gm...>]

Dear colleagues,

Could you please tell me how to create a (multi)reference for the particle
picking?

(I have 3d model of the required particle)

Thank you!

Sincerely,
Dmitry

Re: [scipion-users] Unfilter relion 2D resilt class avarages

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

Dear Dmitry,

Just run relion_reconstruct using the data.star file.

Best wishes,
Juha

On Tue, Sep 6, 2016 at 2:17 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> Does anyone know how to remove the default filtering from the class
> averages obtained with 2D Relion alignment?
>
> Thank you.
>
> Sincerely,
> Dmitry
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] Unfilter relion 2D resilt class avarages

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

Dear Dmitry,

I think that in Relion the output class averages are filtered by default
and there is no option to change that in the underlying program. If you
open the images assigned to one class, then you can compute the average,
that is not filter. But this is only for one class, I don't know if you
want to obtain all class averages unfiltered. I think that we could easily
add a protocol which input is SetOfClasses2D (not only from Relion but from
any 2D classification protocol) and then produce the SetOfAverages
unfiltered.

Hope this helps
Jose Miguel.


On Tue, Sep 6, 2016 at 3:17 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> Does anyone know how to remove the default filtering from the class
> averages obtained with 2D Relion alignment?
>
> Thank you.
>
> Sincerely,
> Dmitry
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] Unfilter relion 2D resilt class avarages

[Dmitry S. <sem...@gm...>]

Dear colleagues,



Does anyone know how to remove the default filtering from the class
averages obtained with 2D Relion alignment?

Thank you.

Sincerely,
Dmitry