scipion-users — Mailing list for Scipion users

[scipion-users] auto-refinement for 2D

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

Dear colleagues,


*? --> auto-refinement for 2D*


We work a lot with negative staining samples doing classification (in
relion 2D) and getting 2D projection average classes.


It might be possible to* improve 2D results* doing *auto-refinement* step
(for 2D).


If yes how can we do that?


I tried to use dataset and created 2D mrc (vol) file as a reference but the
program ended up with some errors.



Dear colleagues do you have any ideas about that possibility ?



Sincerely,

Dmitry

[scipion-users] about RCT-Can I generate a tilted particle set according to an untilted class set?

[ZhuLi <ga...@16...>]

Dear colleagues，


When I did RCT with scipion, I found that it could only generate volumes according to the classified untilted sets (like what you only need to import in the " Random Conical Tilt" menu are the tilt_pairs and Good_classes files ). Since after viewing those volumes, I need to merge a few classes to generate a better volume which may come from the same conformation. Then, what should I do to extract and merge those tilted particles from corresponding classes? (as you know, the classes were generated from untilted particles.) 


Hope I described my question clearly.


Thanks.


Liz

Re: [scipion-users] tiff2mrc

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

Dear Dmitry,

Currently there is no protocol in scipion to convert/save file formats.

Actually, Scipion does it all the time but we never exposed this in the 
workflow as a protocol.


You can use Xmipp programs to do this through scipion command line:


This will print the very detailed help page:
*scipion xmipp_image_convert*

An example could be:
*scipion xmipp_image_convert -i ~/Desktop/mic.tif -o mic.mrc*

We recently discuss about adding a convert/export protocol in Scipion, 
could you please comment on your particular use case. It may help to 
decide whether to create it or not?



On 09/01/17 11:45, Dmitry Semchonok wrote:
> Dear colleagues,
>
> Is is possible to save/convert tiff image to mrc using SCIPION?
>
> Sincerely,
> Dmitry
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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>
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[scipion-users] tiff2mrc

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

Dear colleagues,

Is is possible to save/convert tiff image to mrc using SCIPION?

Sincerely,
Dmitry

Re: [scipion-users] Regarding running protocol on cluster

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

Thank you all! Great job.

Pablo

Scipion Team.


On 26/12/16 03:31, ashutosh srivastava wrote:
> Dear Grigory and Daniel
>
> Thank you so much for the help. It's working perfectly now.
>
> Best Regards
> Ashutosh
>
> On Sat, Dec 24, 2016 at 6:59 PM, Daniel Luque Buzo <dl...@is... 
> <mailto:dl...@is...>> wrote:
>
>     Hello Ashutosh,
>
>     Find attached  he hosts.conf file of out SGE cluster. The file is
>     based scipion wiki example that Grigory pointed.
>
>     The module lines are specific of our cluster (if you do not use
>     module to manage environments/versions in you cluster should not
>     be necessary).
>
>     When we started to configure our cluster, we had the same problem
>     for using more than one node but the problem was related with the
>     parallel environment configuration of the cluster (named orte in
>     our case).
>
>     Hope it helps!
>
>     Best Regards
>     --
>     Daniel Luque Buzo
>     Unidad de Microscopía Electrónica y Confocal
>     Centro Nacional de Microbiología - ISCIII
>     Carretera de Majadahonda - Pozuelo, Km. 2.200
>     28220 - Majadahonda (Madrid)
>     Tel: +34 91 822 39 71 <tel:+34%20918%2022%2039%2071>
>     e-mail: dl...@is... <mailto:dl...@is...>​​
>
>
>     [localhost]
>     PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
>     MANDATORY = 2
>     NAME = OGE
>     CANCEL_COMMAND = qdel %_(JOB_ID)s
>     CHECK_COMMAND = qstat -j %_(JOB_ID)s
>     SUBMIT_COMMAND = qsub %_(JOB_SCRIPT)s
>     SUBMIT_PREFIX = scipion
>     SUBMIT_TEMPLATE = #!/bin/bash
>         ###====================================================###
>         #$ -V
>         #$ -S /bin/bash
>         #$ -cwd ### Use the current working directory
>         #$ -N scipion%_(JOB_NAME)s ### Job name
>         #$ -q %_(JOB_QUEUE)s ### Queue name
>         #$ -pe %_(JOB_PE)s %_(JOB_SLOTS)s
>         #$ -j y ### Merge stdin and stdout
>         ###=======================================================#
>         module load Python/python-2.7.11
>         module load OpenMPI/openmpi-1.10.0
>         ##module load scipion-1.0.0
>         %_(JOB_COMMAND)s
>
>     QUEUES = { "all.q": [
>                          ["JOB_SLOTS","20","Select the proper number
>     of cores"],
>                          ["JOB_PE","orte","Parallel Enviroment
>     (PE)","Select the proper Parallel Enviroment (orte)"]
>                         ]
>              }
>
>
>
>>     El 24 dic 2016, a las 10:01, Grigory Sharov
>>     <sha...@gm... <mailto:sha...@gm...>>
>>     escribió:
>>
>>     Hello Ashutosh,
>>
>>     in scipion wiki there is an example for SGE batch system. You
>>     might check it out and give it a try:
>>
>>     https://github.com/I2PC/scipion/wiki/Host-Configuration
>>     <https://github.com/I2PC/scipion/wiki/Host-Configuration>
>>
>>     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... <mailto:sh...@ig...>
>>
>>     On Sat, Dec 24, 2016 at 2:25 AM, ashutosh srivastava
>>     <ash...@gm... <mailto:ash...@gm...>> wrote:
>>
>>         Dear Scipion Users
>>
>>         I am analysing ~65000 particles in SPA protocol. I am trying
>>         to do this on a cluster which uses SGE as job scheduler.
>>         Since the hosts.conf file is provided for PBS/Torque, I tried
>>         converting it into SGE type script but it failed in using
>>         more than one nodes. So I went ahead and used a bash
>>         jobscript to run the ML2D in the following way
>>
>>         #!/bin/bash
>>         #$ -N classification_2d
>>         #$ -pe openmpi 96
>>         #$ -o pass
>>         #$ -e error
>>         #$ -cwd
>>         #$ -q BLAB
>>         export MPIDIR=/opt/tools/mpi/openmpi-1.10.2-gcc4.4.7/bin
>>         $MPIDIR/mpirun -machinefile $TMPDIR/machines -np $NSLOTS
>>         /opt/tools/scipion/scipion xmipp_mpi_ml_align2d -i
>>         input/particles65818_export.st
>>         <http://particles65818_export.st/>k --nref 200 --fast --oroot
>>         output/ml2d --mirror
>>
>>         This runs fine, generating following files
>>         ml2dclasses.stk
>>         ml2dclasses.xmd
>>         ml2dextra (folder containing iteration data)
>>         ml2d_images_average.xmp
>>         ml2dimages.xmd
>>
>>         However I am having trouble now to write a similar script for
>>         generating initial volume using RANSAC.
>>         Is there a way to use the protocol_ransac.py in a script
>>         similar to one mentioned above? If not then could some one
>>         guide me regarding this?
>>         Apart from this I would also like to know as to how I can
>>         import the classes generated as mentioned above to scipion
>>         gui to visualize them.
>>
>>         Thank you
>>
>>         Best Regards
>>         Ashutosh
>>
>>
>>
>>         ------------------------------------------------------------------------------
>>         Developer Access Program for Intel Xeon Phi Processors
>>         Access to Intel Xeon Phi processor-based developer platforms.
>>         With one year of Intel Parallel Studio XE.
>>         Training and support from Colfax.
>>         Order your platform today.http://sdm.link/intel
>>         _______________________________________________
>>         scipion-users mailing list
>>         sci...@li...
>>         <mailto:sci...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>>         <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>>
>>
>>     ------------------------------------------------------------------------------
>>     Developer Access Program for Intel Xeon Phi Processors
>>     Access to Intel Xeon Phi processor-based developer platforms.
>>     With one year of Intel Parallel Studio XE.
>>     Training and support from Colfax.
>>     Order your platform
>>     today.http://sdm.link/intel_______________________________________________
>>     <http://sdm.link/intel_______________________________________________>
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>>     <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
>     ************************* AVISO LEGAL *************************
>     Este mensaje electrónico está dirigido exclusivamente a sus
>     destinatarios, pudiendo contener documentos anexos de carácter
>     privado y confidencial. Si por error ha recibido este mensaje y no
>     se encuentra entre los destinatarios, por favor no use, informe,
>     distribuya, imprima o copie su contenido por ningún medio. Le
>     rogamos lo comunique al remitente y borre completamente el mensaje
>     y sus anexos. El Instituto de Salud Carlos III no asume ningún
>     tipo de responsabilidad legal por el contenido de este mensaje
>     cuando no responda a las funciones atribuidas al remitente del
>     mismo por la normativa vigente.
>
>
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/intel
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Regarding running protocol on cluster

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

Dear Grigory and Daniel

Thank you so much for the help. It's working perfectly now.

Best Regards
Ashutosh

On Sat, Dec 24, 2016 at 6:59 PM, Daniel Luque Buzo <dl...@is...> wrote:

> Hello Ashutosh,
>
> Find attached  he hosts.conf file of out SGE cluster. The file is based
> scipion wiki example that Grigory pointed.
>
> The module lines are specific of our cluster (if you do not use module to
> manage environments/versions in you cluster should not be necessary).
>
> When we started to configure our cluster, we had the same problem for
> using more than one node but the problem was related with the parallel
> environment configuration of the cluster (named orte in our case).
>
> Hope it helps!
>
> Best Regards
> --
> Daniel Luque Buzo
> Unidad de Microscopía Electrónica y Confocal
> Centro Nacional de Microbiología - ISCIII
> Carretera de Majadahonda - Pozuelo, Km. 2.200
> 28220 - Majadahonda (Madrid)
> Tel: +34 91 822 39 71 <+34%20918%2022%2039%2071>
> e-mail: dl...@is...​​
>
>
> [localhost]
> PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
> MANDATORY = 2
> NAME = OGE
> CANCEL_COMMAND = qdel %_(JOB_ID)s
> CHECK_COMMAND = qstat -j %_(JOB_ID)s
> SUBMIT_COMMAND = qsub %_(JOB_SCRIPT)s
> SUBMIT_PREFIX = scipion
> SUBMIT_TEMPLATE = #!/bin/bash
>     ###====================================================###
>     #$ -V
>     #$ -S /bin/bash
>     #$ -cwd ### Use the current working directory
>     #$ -N scipion%_(JOB_NAME)s ### Job name
>     #$ -q %_(JOB_QUEUE)s ### Queue name
>     #$ -pe %_(JOB_PE)s %_(JOB_SLOTS)s
>     #$ -j y ### Merge stdin and stdout
>     ###=======================================================#
>
>     module load Python/python-2.7.11
>     module load OpenMPI/openmpi-1.10.0
>     ##module load scipion-1.0.0
>     %_(JOB_COMMAND)s
>
> QUEUES = { "all.q": [
>                      ["JOB_SLOTS","20","Select the proper number of
> cores"],
>                      ["JOB_PE","orte","Parallel Enviroment (PE)","Select
> the proper Parallel Enviroment (orte)"]
>                     ]
>          }
>
>
>
> El 24 dic 2016, a las 10:01, Grigory Sharov <sha...@gm...>
> escribió:
>
> Hello Ashutosh,
>
> in scipion wiki there is an example for SGE batch system. You might check
> it out and give it a try:
>
> https://github.com/I2PC/scipion/wiki/Host-Configuration
>
> 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 Sat, Dec 24, 2016 at 2:25 AM, ashutosh srivastava <ash...@gm...>
> wrote:
>
>> Dear Scipion Users
>>
>> I am analysing ~65000 particles in SPA protocol. I am trying to do this
>> on a cluster which uses SGE as job scheduler. Since the hosts.conf file is
>> provided for PBS/Torque, I tried converting it into SGE type script but it
>> failed in using more than one nodes. So I went ahead and used a bash
>> jobscript to run the ML2D in the following way
>>
>> #!/bin/bash
>> #$ -N classification_2d
>> #$ -pe openmpi 96
>> #$ -o pass
>> #$ -e error
>> #$ -cwd
>> #$ -q BLAB
>> export MPIDIR=/opt/tools/mpi/openmpi-1.10.2-gcc4.4.7/bin
>> $MPIDIR/mpirun -machinefile $TMPDIR/machines -np $NSLOTS
>> /opt/tools/scipion/scipion xmipp_mpi_ml_align2d -i input/
>> particles65818_export.stk --nref 200 --fast --oroot output/ml2d --mirror
>>
>> This runs fine, generating following files
>> ml2dclasses.stk
>> ml2dclasses.xmd
>> ml2dextra (folder containing iteration data)
>> ml2d_images_average.xmp
>> ml2dimages.xmd
>>
>> However I am having trouble now to write a similar script for generating
>> initial volume using RANSAC.
>> Is there a way to use the protocol_ransac.py in a script similar to one
>> mentioned above? If not then could some one guide me regarding this?
>> Apart from this I would also like to know as to how I can import the
>> classes generated as mentioned above to scipion gui to visualize them.
>>
>> Thank you
>>
>> Best Regards
>> Ashutosh
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your platform today.http://sdm.link/intel
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
> ------------------------------------------------------------
> ------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/intel___
> ____________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> ************************* AVISO LEGAL ************************* Este
> mensaje electrónico está dirigido exclusivamente a sus destinatarios,
> pudiendo contener documentos anexos de carácter privado y confidencial. Si
> por error ha recibido este mensaje y no se encuentra entre los
> destinatarios, por favor no use, informe, distribuya, imprima o copie su
> contenido por ningún medio. Le rogamos lo comunique al remitente y borre
> completamente el mensaje y sus anexos. El Instituto de Salud Carlos III no
> asume ningún tipo de responsabilidad legal por el contenido de este mensaje
> cuando no responda a las funciones atribuidas al remitente del mismo por la
> normativa vigente.
>

Re: [scipion-users] Regarding running protocol on cluster

[Daniel L. B. <dl...@is...>]

Hello Ashutosh,

Find attached  he hosts.conf file of out SGE cluster. The file is based scipion wiki example that Grigory pointed.

The module lines are specific of our cluster (if you do not use module to manage environments/versions in you cluster should not be necessary).

When we started to configure our cluster, we had the same problem for using more than one node but the problem was related with the parallel environment configuration of the cluster (named orte in our case).

Hope it helps!

Best Regards
--
Daniel Luque Buzo
Unidad de Microscopía Electrónica y Confocal
Centro Nacional de Microbiología - ISCIII
Carretera de Majadahonda - Pozuelo, Km. 2.200
28220 - Majadahonda (Madrid)
Tel: +34 91 822 39 71
e-mail: dl...@is...<mailto:dl...@is...>​​


[localhost]
PARALLEL_COMMAND = mpirun -np %_(JOB_NODES)d -bynode %_(COMMAND)s
MANDATORY = 2
NAME = OGE
CANCEL_COMMAND = qdel %_(JOB_ID)s
CHECK_COMMAND = qstat -j %_(JOB_ID)s
SUBMIT_COMMAND = qsub %_(JOB_SCRIPT)s
SUBMIT_PREFIX = scipion
SUBMIT_TEMPLATE = #!/bin/bash
    ###====================================================###
    #$ -V
    #$ -S /bin/bash
    #$ -cwd ### Use the current working directory
    #$ -N scipion%_(JOB_NAME)s ### Job name
    #$ -q %_(JOB_QUEUE)s ### Queue name
    #$ -pe %_(JOB_PE)s %_(JOB_SLOTS)s
    #$ -j y ### Merge stdin and stdout
    ###=======================================================#

    module load Python/python-2.7.11
    module load OpenMPI/openmpi-1.10.0
    ##module load scipion-1.0.0
    %_(JOB_COMMAND)s

QUEUES = { "all.q": [
                     ["JOB_SLOTS","20","Select the proper number of cores"],
                     ["JOB_PE","orte","Parallel Enviroment (PE)","Select the proper Parallel Enviroment (orte)"]
                    ]
         }



El 24 dic 2016, a las 10:01, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> escribió:

Hello Ashutosh,

in scipion wiki there is an example for SGE batch system. You might check it out and give it a try:

https://github.com/I2PC/scipion/wiki/Host-Configuration

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...<mailto:sh...@ig...>

On Sat, Dec 24, 2016 at 2:25 AM, ashutosh srivastava <ash...@gm...<mailto:ash...@gm...>> wrote:
Dear Scipion Users

I am analysing ~65000 particles in SPA protocol. I am trying to do this on a cluster which uses SGE as job scheduler. Since the hosts.conf file is provided for PBS/Torque, I tried converting it into SGE type script but it failed in using more than one nodes. So I went ahead and used a bash jobscript to run the ML2D in the following way

#!/bin/bash
#$ -N classification_2d
#$ -pe openmpi 96
#$ -o pass
#$ -e error
#$ -cwd
#$ -q BLAB
export MPIDIR=/opt/tools/mpi/openmpi-1.10.2-gcc4.4.7/bin
$MPIDIR/mpirun -machinefile $TMPDIR/machines -np $NSLOTS /opt/tools/scipion/scipion xmipp_mpi_ml_align2d -i input/particles65818_export.st<http://particles65818_export.st/>k --nref 200 --fast --oroot output/ml2d --mirror

This runs fine, generating following files
ml2dclasses.stk
ml2dclasses.xmd
ml2dextra (folder containing iteration data)
ml2d_images_average.xmp
ml2dimages.xmd

However I am having trouble now to write a similar script for generating initial volume using RANSAC.
Is there a way to use the protocol_ransac.py in a script similar to one mentioned above? If not then could some one guide me regarding this?
Apart from this I would also like to know as to how I can import the classes generated as mentioned above to scipion gui to visualize them.

Thank you

Best Regards
Ashutosh



------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users

************************* AVISO LEGAL ************************* Este mensaje electrónico está dirigido exclusivamente a sus destinatarios, pudiendo contener documentos anexos de carácter privado y confidencial. Si por error ha recibido este mensaje y no se encuentra entre los destinatarios, por favor no use, informe, distribuya, imprima o copie su contenido por ningún medio. Le rogamos lo comunique al remitente y borre completamente el mensaje y sus anexos. El Instituto de Salud Carlos III no asume ningún tipo de responsabilidad legal por el contenido de este mensaje cuando no responda a las funciones atribuidas al remitente del mismo por la normativa vigente.

Re: [scipion-users] Regarding running protocol on cluster

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

Hello Ashutosh,

in scipion wiki there is an example for SGE batch system. You might check
it out and give it a try:

https://github.com/I2PC/scipion/wiki/Host-Configuration

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 Sat, Dec 24, 2016 at 2:25 AM, ashutosh srivastava <ash...@gm...>
wrote:

> Dear Scipion Users
>
> I am analysing ~65000 particles in SPA protocol. I am trying to do this on
> a cluster which uses SGE as job scheduler. Since the hosts.conf file is
> provided for PBS/Torque, I tried converting it into SGE type script but it
> failed in using more than one nodes. So I went ahead and used a bash
> jobscript to run the ML2D in the following way
>
> #!/bin/bash
> #$ -N classification_2d
> #$ -pe openmpi 96
> #$ -o pass
> #$ -e error
> #$ -cwd
> #$ -q BLAB
> export MPIDIR=/opt/tools/mpi/openmpi-1.10.2-gcc4.4.7/bin
> $MPIDIR/mpirun -machinefile $TMPDIR/machines -np $NSLOTS
> /opt/tools/scipion/scipion xmipp_mpi_ml_align2d -i input/
> particles65818_export.stk --nref 200 --fast --oroot output/ml2d --mirror
>
> This runs fine, generating following files
> ml2dclasses.stk
> ml2dclasses.xmd
> ml2dextra (folder containing iteration data)
> ml2d_images_average.xmp
> ml2dimages.xmd
>
> However I am having trouble now to write a similar script for generating
> initial volume using RANSAC.
> Is there a way to use the protocol_ransac.py in a script similar to one
> mentioned above? If not then could some one guide me regarding this?
> Apart from this I would also like to know as to how I can import the
> classes generated as mentioned above to scipion gui to visualize them.
>
> Thank you
>
> Best Regards
> Ashutosh
>
>
>
> ------------------------------------------------------------
> ------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/intel
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] Regarding running protocol on cluster

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

Dear Scipion Users

I am analysing ~65000 particles in SPA protocol. I am trying to do this on
a cluster which uses SGE as job scheduler. Since the hosts.conf file is
provided for PBS/Torque, I tried converting it into SGE type script but it
failed in using more than one nodes. So I went ahead and used a bash
jobscript to run the ML2D in the following way

#!/bin/bash
#$ -N classification_2d
#$ -pe openmpi 96
#$ -o pass
#$ -e error
#$ -cwd
#$ -q BLAB
export MPIDIR=/opt/tools/mpi/openmpi-1.10.2-gcc4.4.7/bin
$MPIDIR/mpirun -machinefile $TMPDIR/machines -np $NSLOTS
/opt/tools/scipion/scipion xmipp_mpi_ml_align2d -i input/
particles65818_export.stk --nref 200 --fast --oroot output/ml2d --mirror

This runs fine, generating following files
ml2dclasses.stk
ml2dclasses.xmd
ml2dextra (folder containing iteration data)
ml2d_images_average.xmp
ml2dimages.xmd

However I am having trouble now to write a similar script for generating
initial volume using RANSAC.
Is there a way to use the protocol_ransac.py in a script similar to one
mentioned above? If not then could some one guide me regarding this?
Apart from this I would also like to know as to how I can import the
classes generated as mentioned above to scipion gui to visualize them.

Thank you

Best Regards
Ashutosh

Re: [scipion-users] Local resolution estimation

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

Dear Dmitry,

this is a very timely question. We have just integrated into the devel 
branch a tool called MonoRes which also measures locally the resolution 
following a different mathematical approach. The paper is almost written 
and will be sent shortly to a journal. If you want to use the method 
before its formal presentation, you may contact Jose Luis Vilas, its author.

Kind regards, Carlos Oscar


On 12/23/16 15:12, Dmitry A. Semchonok wrote:
> Dear colleagues,
>
> What are the local resolution estimation tools we have except resmap?
>
> Sincerely
> Dmitry
>
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/intel
> _______________________________________________
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> 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] Local resolution estimation

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

Dear colleagues,

What are the local resolution estimation tools we have except resmap?

Sincerely
Dmitry

Re: [scipion-users] particle polishing

[Josue G. B. <jos...@gm...>]

Dear Dmitry:
It seems that you have a problem with the RAM memory available in your
cluster. In version 1.0.1 the results of  cross-correlation+Optical Flow
(alignining your movies) are the same as particle polishing, and it is a
simpler way to process the particles. Unfortunately, particle polishing
demands  a huge of RAM memory and time, and depends of your particle
dimensions and the number of particles. The only  way to decrease the
amount of memory without change the dimensions of the images is decreasing
the number of MPI processes (until 1), but, of course, there exist a
minimum... In previous projects I needed a worstation (1node) with 512GB of
RAM to successfully execute particle polish with 3 MPI process (I dont
remember the box size, but no more than 400 pixels). Maybe you can try with
a compilation of relion in single precision.... Can you send me a log error
to see the problem?...
Best Regards, Josue

2016-12-08 16:24 GMT+01:00 Dmitry Semchonok <sem...@gm...>:

> Dear colleagues,
>
> I'm still on the stage of particle polishing (from the frames)
>
>
> What are on average *the setting* that you use for the
>
>
> 1) MPI
>
> 2) nodes/himem - ?
>
> What is on average
>
> *the memory per/core (in himem mode)? *I tried 20480; 40960 = error
>
> I have something around 800 000 frames
>
>
>
>
> Sincerely
> Dmitry
>
> ------------------------------------------------------------
> ------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

[scipion-users] particle polishing

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

Dear colleagues,

I'm still on the stage of particle polishing (from the frames)


What are on average *the setting* that you use for the


1) MPI

2) nodes/himem - ?

What is on average

*the memory per/core (in himem mode)? *I tried 20480; 40960 = error

I have something around 800 000 frames




Sincerely
Dmitry

[scipion-users] Import movies and create stacks

[Weng Ng <we...@ne...>]

Hi All,

I have been trying to import movie frames and create movie stacks at the same time using scipion, but each time it failed after importing with this message :

Traceback (most recent call last):
  File "/dls_sw/apps/scipion/devel/scipion/pyworkflow/protocol/protocol.py", line 182, in run
    self._run()
  File "/dls_sw/apps/scipion/devel/scipion/pyworkflow/protocol/protocol.py", line 234, in _run
    raise Exception('Missing filePaths: ' + ' '.join(missingFiles))
Exception: Missing filePaths:

Does this mean there is an error in the script for this? But I have previously done this without error. Kindly please enlighten me.

Many thanks,
Weng

Re: [scipion-users] particle polishing with movies error

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

Dear Dmitry,

the problem seems to be related to the maximum memory limit for each of 
the working nodes. I'm not familiar with slurm but most queuing systems 
have an option to increase the maximum memory available to each node 
(this also seems to be the case of Slurm, 
https://slurm.schedmd.com/sbatch.html). This should go in Scipion host 
configuration file 
(https://github.com/I2PC/scipion/wiki/Host-Configuration, probably you 
have already edited this file to be able to submit jobs to Slurm).

Regarding threads or mpi, it is not a matter of the GUI interface but 
the program itself. Relion_polishing is implemented using mpi 
parallelization and not threads.

Kind regards, Carlos Oscar


On 12/06/16 13:08, Dmitry Semchonok wrote:
> Dear colleagues,
>
> I have a problem running particle polishing.
>
> Every time I try to run it (with movies) I get an error:
>
> In the run file I have the following notification:
>
> *run.stdout:*
> ....................................
>
> slurmstepd: Exceeded step memory limit at some point....
> .......................................
>
> *Log file:*
>
> Protocol failed: Command 'srun  `which relion_particle_polish_mpi`  
> --i Runs/015602_ProtRelionPolish/extra/relion_it032_data.star --o 
> shiny --angpix 1.108 --movie_frames_running_avg 5 
> --dont_read_old_files --sym c2 --sigma_nb 100 --perframe_highres 3.000 
> --autob_lowres 20.000 --bg_radius 155 --mask 
> Runs/015357_ProtRelionPostprocess/extra/postprocess_automask.mrc ' 
> returned non-zero exit status 137
>
> Any recommendations?
>
> In the gui is only MPI available (no threads).
>
> What are the working settings?
>
> Than you!
>
> Sincerely,
> Dmitry
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
>
>
> _______________________________________________
> 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] particle polishing with movies error

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

Dear colleagues,

I have a problem running particle polishing.

Every time I try to run it (with movies) I get an error:

In the run file I have the following notification:

*run.stdout:*
....................................

slurmstepd: Exceeded step memory limit at some point....
.......................................

*Log file:*

Protocol failed: Command 'srun  `which relion_particle_polish_mpi`  --i
Runs/015602_ProtRelionPolish/extra/relion_it032_data.star --o shiny
--angpix 1.108 --movie_frames_running_avg 5 --dont_read_old_files --sym c2
--sigma_nb 100 --perframe_highres 3.000 --autob_lowres 20.000 --bg_radius
155 --mask Runs/015357_ProtRelionPostprocess/extra/postprocess_automask.mrc
' returned non-zero exit status 137

Any recommendations?

In the gui is only MPI available (no threads).

What are the working settings?

Than you!

Sincerely,
Dmitry

Re: [scipion-users] noisy 3d model, b-factor, post-processing

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

Hello Dmitry,

post-processing in relion is described in its wiki:
http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Analyse_results#Getting_higher_resolution_and_map_sharpening


Did you provide a mask? Increasing B-factor (e.g., -200) strongly enhances
high resolution features including noise, so it's normal.

If your resolution is above 10A I wouldn't use B-sharpening/MTF division
altogether. Also, auto B-factor might simply not work for these cases.

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 Fri, Dec 2, 2016 at 1:57 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> I run the *protocol relion-post-processing* and the result model has some
> noise mainly around the center.
>
>
> The b-factor that was first set to the auto value (how to find out what
> was it precisely for the “auto” settings?)
>
>
> I set the b-factor manually -50, -100, -200
>
>
>
> The less noise was obtained with b-factor = -50
>
> How to get rid of that noise and set the correct b-factor?
>
> There is no such noise in the classification file.
>
>
>
> (K2mtf was taken from relion mrc website)
>
>
>
>
>
>
> Thank you.
>
>
>
> Sincerely,
>
> Dmitry
>
> ------------------------------------------------------------
> ------------------
> 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] noisy 3d model, b-factor, post-processing

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

Dear colleagues,



I run the *protocol relion-post-processing* and the result model has some
noise mainly around the center.


The b-factor that was first set to the auto value (how to find out what was
it precisely for the “auto” settings?)


I set the b-factor manually -50, -100, -200



The less noise was obtained with b-factor = -50

How to get rid of that noise and set the correct b-factor?

There is no such noise in the classification file.



(K2mtf was taken from relion mrc website)






Thank you.



Sincerely,

Dmitry

[scipion-users] particle polishing

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

Dear colleagues,



I try to run particle polishing protocol.



As input I placed 3Dautorefine file.

The program stopped saying –



00155:   There are no images read in: please check your input file...

00156:   File: src/exp_


And after fails saying


Protocol failed: Command 'srun  `which relion_particle_polish_mpi`  --i
Runs/015051_ProtRelionPolish/extra/relion_it032_data.star --o shiny
--angpix 1.108 --movie_frames_running_avg 5 --dont_read_old_files --sym c2
--sigma_nb 100 --perframe_highres 3.000 --autob_lowres 20.000 --bg_radius
160 --mask Runs/014999_ProtRelionPostprocess/extra/postprocess_automask.mrc
' returned non-zero exit status 1



When I in the settings press on eye to see the input – nothing is shown



Is there a solution?

P.s. The postprocessing runs with the same input file with no problems


Sincerely,

Dmitry

Re: [scipion-users] RCT in the initial vol tutorial

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

Dear Elad,

in version 1.0.1, mpi is not fully working. You may try to use only 
threads, or no parallelization at all (thread=1, mpi=1)

Kind regards, Carlos Oscar


On 11/28/16 19:56, Elad Binshtein wrote:
> Hi All,
>
> I still try to run the xmipp RCT wiyh no luck.
>
> I have this error with the mpi4py in the terminal:
>
> Running runJobMPISlave:  1
> Traceback (most recent call last):
>   File 
> "/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/apps/pw_protocol_mpirun.py", 
> line 57, in <module>
>     runJobMPISlave(comm)
>   File 
> "/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/utils/mpi.py", 
> line 107, in runJobMPISlave
>     done, command = req_recv.test()
>   File "Request.pyx", line 237, in mpi4py.MPI.Request.test 
> (src/mpi4py.MPI.c:52898)
>   File "pickled.pxi", line 401, in mpi4py.MPI.PyMPI_test 
> (src/mpi4py.MPI.c:31080)
> mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated
>
> our IT try to fix it together with SBgrid and it not working. Do 
> anyone have this error?
>
> Thanks,
>
>
> On Tue, Nov 1, 2016 at 3:41 PM, Grigory Sharov 
> <sha...@gm... <mailto:sha...@gm...>> wrote:
>
>     Hi,
>
>     the thing is that protocol runs with mpi=2 and 1 thread (by
>     default in the protocol, thread number is not taken from GUI) and
>     prints all output to console and not to run.stdout.
>
>     Elad, in principle it should still run (however slowly), you could
>     check the output in the console where you launched scipion (if it
>     was done interactively) or the output log file from the job
>     submission system on your cluster (if you run it on cluster).
>
>     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... <mailto:sh...@ig...>
>
>     On Tue, Nov 1, 2016 at 9:12 PM, Carlos Oscar Sorzano
>     <co...@cn... <mailto:co...@cn...>> wrote:
>
>         Dear Elad,
>
>         can you send the log so that we can better see what may be
>         happening? If you attach a screenshot of the project, we may
>         try to figure out the workflow you have followed.
>
>         Kind regards, Carlos Oscar
>
>
>         On 11/01/16 17:05, Elad Binshtein wrote:
>>         Hi,
>>         I'm try to go through the  initial vol tutorial and in the
>>         lass step EMAN and ransac is work good I can not run the
>>         xmipp RCT protocol (no error on the run log just stuck on
>>         step 1/8)
>>         any suggestion?
>>
>>         Thanks
>>
>>         -- 
>>         ________________________________
>>         Elad Binshtein, Ph.D.
>>         Cryo EM specialist - staff scientist
>>         Center for Structure Biology (CSB)
>>         Vanderbilt University
>>         Nashville, TN
>>         Mobile: +1-615-481-4408 <tel:%2B1-615-481-4408>
>>         E-Mail: el...@gm... <mailto:el...@gm...>
>>         ________________________________
>>
>>
>>         ------------------------------------------------------------------------------
>>         Developer Access Program for Intel Xeon Phi Processors
>>         Access to Intel Xeon Phi processor-based developer platforms.
>>         With one year of Intel Parallel Studio XE.
>>         Training and support from Colfax.
>>         Order your platform today.http://sdm.link/xeonphi
>>
>>         _______________________________________________
>>         scipion-users mailing list
>>         sci...@li...
>>         <mailto:sci...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>>         <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
>         -- 
>         ------------------------------------------------------------------------
>         Carlos Oscar Sánchez Sorzano                  e-mail:co...@cn... <mailto:co...@cn...>
>         Biocomputing unithttp://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
>         ------------------------------------------------------------------------
>
>         ------------------------------------------------------------------------------
>         Developer Access Program for Intel Xeon Phi Processors Access
>         to Intel Xeon Phi processor-based developer platforms. With
>         one year of Intel Parallel Studio XE. Training and support
>         from Colfax. Order your platform today.
>         http://sdm.link/xeonphi
>         _______________________________________________ scipion-users
>         mailing list sci...@li...
>         <mailto:sci...@li...>
>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>         <https://lists.sourceforge.net/lists/listinfo/scipion-users> 
>
> -- 
> ________________________________ Elad Binshtein, Ph.D.
> Cryo EM specialist - staff scientist Center for Structure Biology 
> (CSB) MCN Room 1207 Vanderbilt University Nashville, TN Office: 
> +1-615-322-4671 Mobile: +1-615-481-4408E-Mail: el...@gm... 
> <mailto:el...@gm...> ________________________________
-- 
------------------------------------------------------------------------
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
------------------------------------------------------------------------

Re: [scipion-users] RCT in the initial vol tutorial

[Elad B. <el...@gm...>]

Hi All,

I still try to run the xmipp RCT wiyh no luck.

I have this error with the mpi4py in the terminal:

Running runJobMPISlave:  1
Traceback (most recent call last):
  File
"/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/apps/pw_protocol_mpirun.py",
line 57, in <module>
    runJobMPISlave(comm)
  File
"/home/sbgrid/programs/x86_64-linux/scipion/1.0.1/pyworkflow/utils/mpi.py",
line 107, in runJobMPISlave
    done, command = req_recv.test()
  File "Request.pyx", line 237, in mpi4py.MPI.Request.test
(src/mpi4py.MPI.c:52898)
  File "pickled.pxi", line 401, in mpi4py.MPI.PyMPI_test
(src/mpi4py.MPI.c:31080)
mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated

our IT try to fix it together with SBgrid and it not working. Do anyone
have this error?

Thanks,


On Tue, Nov 1, 2016 at 3:41 PM, Grigory Sharov <sha...@gm...>
wrote:

> Hi,
>
> the thing is that protocol runs with mpi=2 and 1 thread (by default in the
> protocol, thread number is not taken from GUI) and prints all output to
> console and not to run.stdout.
>
> Elad, in principle it should still run (however slowly), you could check
> the output in the console where you launched scipion (if it was done
> interactively) or the output log file from the job submission system on
> your cluster (if you run it on cluster).
>
> 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 Tue, Nov 1, 2016 at 9:12 PM, Carlos Oscar Sorzano <co...@cn...>
> wrote:
>
>> Dear Elad,
>>
>> can you send the log so that we can better see what may be happening? If
>> you attach a screenshot of the project, we may try to figure out the
>> workflow you have followed.
>>
>> Kind regards, Carlos Oscar
>>
>> On 11/01/16 17:05, Elad Binshtein wrote:
>>
>> Hi,
>> I'm try to go through the  initial vol tutorial and in the lass step EMAN
>> and ransac is work good I can not run the xmipp RCT protocol (no error on
>> the run log just stuck on step 1/8)
>> any suggestion?
>>
>> Thanks
>>
>> --
>> ________________________________
>> Elad Binshtein, Ph.D.
>> Cryo EM specialist - staff scientist
>> Center for Structure Biology (CSB)
>> Vanderbilt University
>> Nashville, TN
>> Mobile: +1-615-481-4408
>> E-Mail: el...@gm...
>> ________________________________
>>
>>
>> ------------------------------------------------------------------------------
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your platform today. http://sdm.link/xeonphi
>>
>>
>>
>> _______________________________________________
>> scipion-users mailing lis...@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
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from Colfax.
>> Order your platform today. http://sdm.link/xeonphi
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>


-- 
________________________________
Elad Binshtein, Ph.D.
Cryo EM specialist - staff scientist
Center for Structure Biology (CSB)
MCN Room 1207
Vanderbilt University
Nashville, TN
Office: +1-615-322-4671
Mobile: +1-615-481-4408
E-Mail: el...@gm...
________________________________

Re: [scipion-users] protocol grigoriefflab - unblur

[Jose M. C. <ca...@cn...>]

Dear Dimitry,

Regarding local and non-local correction, like Optical Flow, in the context
of last year Map Challenge, we could show that Optical Flow always produced
equal or better results than non-local approach. At the time we did not use
dose compensation, which should improuve on top.

Josue Gomez has all the test data on our side, that were indeed compiled
but never published

Wbw..JM

On Wed, Nov 23, 2016 at 7:35 AM, Carlos Oscar Sorzano <co...@cn...>
wrote:

> Dear Dmitry,
>
> as far as I remember there is no serious comparison about different
> strategies of dose compensation, frame alignment (either at the level of
> micrograph as in cross correlation/optical flow or at the level of
> particle, polishing). Assuming that any combination is equivalent to any
> other combination is not reasonable, but unfortunately, I don't have an
> answer to which strategy is the best. Each one showed in their respective
> publications, that that action alone was improving resolution, but there
> has been nothing on the comparison or the combination of them.
>
> Kind regards, Carlos Oscar
>
> On 22/11/2016 11:55, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> 1 more question
>
> How do you use the *protocol grigoriefflab - unblur*?
>
> After the *movie alignment protocol*?
>
> How important is to use this protocol?
>
> Isn't the particle polishing will in a way do the same?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> scipion-users mailing lis...@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 mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>


-- 
Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049 Madrid, Spain


Cell: +34639197980

Re: [scipion-users] protocol grigoriefflab - unblur

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

Hi Dmitry,

You could look at the following paper
https://www.ncbi.nlm.nih.gov/pubmed/27572725 that compares all popular
methods of movie alignment except the most recent motioncor2 program

On Nov 22, 2016 13:55, "Dmitry Semchonok" <sem...@gm...> wrote:

> Dear colleagues,
>
> 1 more question
>
> How do you use the *protocol grigoriefflab - unblur*?
>
> After the *movie alignment protocol*?
>
> How important is to use this protocol?
>
> Isn't the particle polishing will in a way do the same?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
> ------------------------------------------------------------
> ------------------
>
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> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] protocol grigoriefflab - unblur

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

Dear Dmitry,

as far as I remember there is no serious comparison about different 
strategies of dose compensation, frame alignment (either at the level of 
micrograph as in cross correlation/optical flow or at the level of 
particle, polishing). Assuming that any combination is equivalent to any 
other combination is not reasonable, but unfortunately, I don't have an 
answer to which strategy is the best. Each one showed in their 
respective publications, that that action alone was improving 
resolution, but there has been nothing on the comparison or the 
combination of them.

Kind regards, Carlos Oscar


On 22/11/2016 11:55, Dmitry Semchonok wrote:
> Dear colleagues,
>
> 1 more question
>
> How do you use the *protocol grigoriefflab - unblur*?
>
> After the *movie alignment protocol*?
>
> How important is to use this protocol?
>
> Isn't the particle polishing will in a way do the same?
>
>
> Thank you
>
> 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
------------------------------------------------------------------------

Re: [scipion-users] Improving the workflow that was done

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

Dear Dmitry,

What version of Scipion are you using? v1.0.x ?

In that version cross-correlation global alignment (CC) was in the same
protocol of optical flow local alignment (OF).
In the devel version we have decoupled different movie alignment protocols,
but this will be for the next release.
If you used the v1.0, you will need to relaunch a "copy" of the movie
alignment job and then combine both CC + OF.

If you have already estimated the CTF for the first workflow, then you
could reuse that when re-extracting particles
from the new aligned micrographs. Or you can just re-estimate with Xmipp or
any other program if you like...you should
start a new job as usual and use the new micrographs as input.

Hope this helps
Jose Miguel


On Tue, Nov 22, 2016 at 11:04 AM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
> I used protocol xmipp3 - movie alignment but only cross-correlation
> correction.
>
> But now I would like to add optical correction.
>
> Is there a way to redo this step?
>
> I already processed till the final 3d model....
>
>
> Also I would like to incert xmipp - ctf extimation protocol inbetween
>
> grigotieflab and particle picking
>
> Is that any possible?
>
>
>
>
> Sincerely,
> Dmitry
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>