scipion-users — Mailing list for Scipion users

Re: [scipion-users] OpenCV not found for Xmipp

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

Hi David, Wolfgang and Scipion users,

Regarding the first question of why the openCV code of Xmipp is not
compailing when OpenCV is in a alternate location, Xmipp needs the headers
files of OpenCV to compile that part of the code, thus you must have
installed the devel version of the OpenCV package and, also, the include
folder of the openCV must be seeable during the compilation time.

Regarding the libtiff versions fight, yes Scipion has libtiff5, then if
other libtiff is used to compile the system's openCV, it will fail.

Both issues might be fixed by installing OpenCV inside Scipion via

$ cd $SCIPION_HOME
$ ./scipion install opencv -j N

where N is the number of processors (take into account that this
installation takes a while, thus the bigger N is better).

NOTE: Regarding the OpenCV inside Scipion, we have using the OpenCV-v2.4.13
by default and we have checked that it works fine for Centos7 and Ubuntu16.
However, for Ubuntu 18, we have observed that the OpenCV-v3.4.1 should be
used. Therefore, if you use Ubuntu18, you should edit the
$SCIPION_HOME/config/scipion.conf in such a way that OPENCV_VER=3.4.1 and
then install opencv using the command above (this only works if Scipion is
installed from sources, not from binaries).


Finally, just to note that OpenCV is used by Xmipp only for two non
critical protocols (Optical Alignment and Enric -former Volume
Homogenizer-). Therefore, if you don't need this two protocols and it still
not working even with the hints pointed out above, the OpenCV code in Xmipp
can be ignored by editing $SCIPION_HOME/config/scipion.conf in such a way
that OPENCV=False and, then, trying to compile Xmipp again.


I hope tht it will help and my appologies for the late reply.


Thanks for reporting!

<http://ucm.es/>

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

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On Tue, May 28, 2019 at 6:12 PM Hoover, David (NIH/CIT) [E] via
scipion-users <sci...@li...> wrote:

> No.  I've been attempting to compile Xmipp from source, but that is even
> harder.
>
> David Hoover
> HPC @ NIH
>
> On 5/27/2019 11:28 AM, Pablo Conesa wrote:
> > Hi David! Have we ever replied to you with a solution?
> >
> > On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
> >> Hi,
> >>
> >> I recently installed Scipion 2.0 and all the plugins, and attempted to
> run the tutorials.  We have OpenCV installed in an alternate location, and
> I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting
> complaints that it is not installed, and that I should fix this and
> reinstall Xmipp.
> >>
> >> How does Xmipp know where OpenCV is?  Can I set a configuration
> somewhere stating where it is located?
> >>
> >> David Hoover
> >> HPC @ NIH
> >>
> >>
> >> _______________________________________________
> >> scipion-users mailing list
> >> sci...@li...
> >> https://lists.sourceforge.net/lists/listinfo/scipion-users
> >
> >
> > _______________________________________________
> > scipion-users mailing list
> > sci...@li...
> > https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] OpenCV not found for Xmipp

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

<div dir='auto'>Try to set OPENCV to False in &lt;scipion home&gt;/config/scipion.conf<div dir="auto"><br></div><div dir="auto">If there are problems with OPENCV, this is the simplest way to fix it. There'll be 2 methods missing but they are not commonly used.</div></div>

Re: [scipion-users] OpenCV not found for Xmipp

[Hoover, D. (NIH/C. [E] <hoo...@hp...>]

No.  I've been attempting to compile Xmipp from source, but that is even harder.

David Hoover
HPC @ NIH

On 5/27/2019 11:28 AM, Pablo Conesa wrote:
> Hi David! Have we ever replied to you with a solution?
> 
> On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
>> Hi,
>>
>> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials.  We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp.
>>
>> How does Xmipp know where OpenCV is?  Can I set a configuration somewhere stating where it is located?
>>
>> David Hoover
>> HPC @ NIH
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> 
> 
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] OpenCV not found for Xmipp

[Lugmayr, W. <w.l...@uk...>]

hi,

no, but i have a similar problem.

the centos7 opencv is compiled against libtiff4 but scipion2 comes with libtiff5. 
therefore some of the new xmipp executables cannot be linked and they are also not available in the centos binary plugin package.

cheers,
wolfgang


----- Original Message -----
From: "Pablo Conesa" <pc...@cn...>
To: "Hoover, David (NIH/CIT) [E] via scipion-users" <sci...@li...>
Sent: Monday, 27 May, 2019 17:28:28
Subject: Re: [scipion-users] OpenCV not found for Xmipp

Hi David! Have we ever replied to you with a solution?

On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
> Hi,
>
> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials.  We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp.
>
> How does Xmipp know where OpenCV is?  Can I set a configuration somewhere stating where it is located?
>
> David Hoover
> HPC @ NIH
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users


_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] OpenCV not found for Xmipp

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

Hi David! Have we ever replied to you with a solution?

On 23/5/19 17:09, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
> Hi,
>
> I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials.  We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp.
>
> How does Xmipp know where OpenCV is?  Can I set a configuration somewhere stating where it is located?
>
> David Hoover
> HPC @ NIH
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] How to export files?

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

Hi Matt Harrington (disambiguation needed now ;)

As Matt Hutchison pointed out, you can created a new Scipion project for
each session, or more than one per session.
Then you could manually import templates for the pre-processing steps. Some
of these task are ease/automate by
the use of "session wizards", that are basically Python scripts (or whole
apps) that use the Scipion API to setup
in some case folders structures, basic initial parameters and the creation
of the project template. So, between one user
and the next one, should not be any issue, unless you run out of disk space
or you want to prevent one uses to see
the data from the previous one...in which case I think it should make more
sense having different OS users.

We have created different session wizards to setups things
and create the project template...taking care of some data management. In
our case (CryoEM facility in Stockholm), the wizard also
fetch information from the Booking system and the Application portal, where
we have information
about the project that the current session belongs (and the PI that should
be invoiced). These wizards
are ad-hoc, so no general for every place... you can see the Stockholm one
here: https://github.com/delarosatrevin/scipion-session
(See also attached image)

And some instructions for the internal users about how to use it:
https://github.com/delarosatrevin/scipion-session/wiki/Instructions-to-use-the-Session-Wizard-at-SciLifeLab
Grigory Sharov have also created one for the LMB:
https://github.com/azazellochg/scipion-session-lmb
And the web one being used in Madrid:
https://github.com/I2PC/EMadmin/tree/master

Although Scipion has been designed with extensibility in mind (through
adding new plugins, protocols, viewers, etc),
creating a new plugin for data transfer seems a bit overkilling. My
colleagues in Madrid has developed a protocol (or
script) to transfer the project data to an external hdd while the
pre-processing is going on. I haven't found it, but
they might comment more on this. If it is no longer used there, could be a
better starting point for your use case.

You might want to take a look at our paper about using Scipion for CryoEM
facilities here:
https://www.sciencedirect.com/science/article/pii/S1047847718302740

Best,
Jose Miguel



On Fri, May 24, 2019 at 9:19 PM Hutchison, Matt (NIH/NCI) [C] via
scipion-users <sci...@li...> wrote:

> Matt,
>
>
>
> The overall layout sounds similar to what we deal with here.  In our case,
> we have a project template that is executed using the scripting interface,
> so we run the same tasks during each imaging session but they’re created as
> separate projects at execution time, with a few variables set in the
> template (project name, pixel size, paths, ctf parameters).  It’s also
> possible to do something similar in the GUI by creating a project that can
> be imported w/copy at the start of each session to create a new project
> each time with the same basic template.  We use v1.2.1 right now, but I
> think that both of these are still available in v2.0.
>
>
>
> Also, can you share what precisely you’re doing when you see files being
> deleted from the project?  That sounds odd to me.
>
>
>
> *Matt Hutchison (Contractor)*
>
> Software Developer
>
> National Cryo-EM Facility
>
> Cancer Research Technology Program
>
> Frederick National Laboratory for Cancer Research
>
> Leidos Biomedical Research Inc.
>
> PO Box B Frederick, MD 21702
>
> Phone: 301-360-3483
>
> Email: tho...@ni...
>
>
>
> *From: *Matt Harrington <ma...@ms...>
> *Reply-To: *Mailing list for Scipion users <
> sci...@li...>
> *Date: *Friday, May 24, 2019 at 2:06 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] How to export files?
>
>
>
> On Fri, May 24, 2019 at 9:23 AM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>
>
> If I understood correctly your question, you are talking more about
> transferring the data of a pre-processing project.
>
>
>
> Correct.  Thanks for your thoughts.  Here are a few more details.  We run
> under a shared user account, and we're expecting that each person will use
> the same Scipion pre-processing pipeline.  It sounds like users should
> manually copy drift-corrected files out of the project folder before the
> next user comes along.  Otherwise, they'll be deleted.
>
>
>
> Managing data transfer/policies is beyond the scope of Scipion...and it is
> almost impossible to do it in a general (and robust) way that serve all the
> different situations.
>
>
>
> The good thing is that we can create our own export plug-in.  I assume
> this contains all we need to know:
> https://scipion-em.github.io/docs/docs/developer/creating-a-plugin.
>
>
>
> Matt
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] How to export files?

[Hutchison, M. (NIH/N. [C] <tho...@ni...>]

Matt,

The overall layout sounds similar to what we deal with here.  In our case, we have a project template that is executed using the scripting interface, so we run the same tasks during each imaging session but they’re created as separate projects at execution time, with a few variables set in the template (project name, pixel size, paths, ctf parameters).  It’s also possible to do something similar in the GUI by creating a project that can be imported w/copy at the start of each session to create a new project each time with the same basic template.  We use v1.2.1 right now, but I think that both of these are still available in v2.0.

Also, can you share what precisely you’re doing when you see files being deleted from the project?  That sounds odd to me.

Matt Hutchison (Contractor)
Software Developer
National Cryo-EM Facility
Cancer Research Technology Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research Inc.
PO Box B Frederick, MD 21702
Phone: 301-360-3483
Email: tho...@ni...<mailto:tho...@ni...>

From: Matt Harrington <ma...@ms...>
Reply-To: Mailing list for Scipion users <sci...@li...>
Date: Friday, May 24, 2019 at 2:06 PM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] How to export files?

On Fri, May 24, 2019 at 9:23 AM Jose Miguel de la Rosa Trevin <del...@gm...<mailto:del...@gm...>> wrote:

If I understood correctly your question, you are talking more about transferring the data of a pre-processing project.

Correct.  Thanks for your thoughts.  Here are a few more details.  We run under a shared user account, and we're expecting that each person will use the same Scipion pre-processing pipeline.  It sounds like users should manually copy drift-corrected files out of the project folder before the next user comes along.  Otherwise, they'll be deleted.

Managing data transfer/policies is beyond the scope of Scipion...and it is almost impossible to do it in a general (and robust) way that serve all the different situations.

The good thing is that we can create our own export plug-in.  I assume this contains all we need to know: https://scipion-em.github.io/docs/docs/developer/creating-a-plugin.

Matt

Re: [scipion-users] How to export files?

[Matt H. <ma...@ms...>]

On Fri, May 24, 2019 at 9:23 AM Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

If I understood correctly your question, you are talking more about
> transferring the data of a pre-processing project.
>

Correct.  Thanks for your thoughts.  Here are a few more details.  We run
under a shared user account, and we're expecting that each person will use
the same Scipion pre-processing pipeline.  It sounds like users should
manually copy drift-corrected files out of the project folder before the
next user comes along.  Otherwise, they'll be deleted.


> Managing data transfer/policies is beyond the scope of Scipion...and it is
> almost impossible to do it in a general (and robust) way that serve all the
> different situations.
>

The good thing is that we can create our own export plug-in.  I assume this
contains all we need to know:
https://scipion-em.github.io/docs/docs/developer/creating-a-plugin.

Matt

Re: [scipion-users] How to export files?

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

Hi Matt,

Just one clarification...what Gregory mention about 'export protocols' is
related to exporting some of the jobs executing in Scipion as ready-to-use
files for importing into orther programs (mainly Relion right now).

If I understood correctly your question, you are talking more about
transferring the data of a pre-processing project. Scipion projects are
self-contained folders (except for initial import that are symbolic links
that can be broken...and restored). So, it is up to each facility how to
manage the Scipion data generated for one session. In our case in
Stockholm, we store the raw files and the pre-processing project for one
month. During that time, users are responsible for connecting to our server
and copy the data back. We remove session data that is more than one month
older.

Managing data transfer/policies is beyond the scope of Scipion...and it is
almost impossible to do it in a general (and robust) way that serve all the
different situations.

Hope this helps,
Best,
Jose Miguel




On Fri, May 24, 2019 at 5:36 PM Gregory Sharov <sha...@gm...>
wrote:

> Hello Matt,
>
> Thank you for your interest! At the moment there are two protocols (relion
> - export ctf and relion - export particles) that can create a star file for
> importing into Relion. You can find them by using Ctrl+F, it's true they
> are not in export section at the moment (to be fixed).
> If you also want to move the data files outside the project you will have
> to fix the produced star file (awk can do it neatly).
>
> The processed data is kept unless you overwrite/delete the project.
> Unless, of course, if you plan to remove the old scipion projects as soon
> as the session if finished.
>
> Hope this helps,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267542 <+44%201223%20267542>
> e-mail: gs...@mr...
>
>
> On Fri, May 24, 2019 at 4:24 PM Matt Harrington <ma...@ms...> wrote:
>
>>
>> We're evaluating Scipion for use by our facility, not necessarily for use
>> by individual users.  I recently had a demo and was left with one
>> question.  It's not clear how to export processed data to final
>> destination.  We have a simple pipeline of Import -> MotionCor2 ->
>> Ctffind.  It appears that processed files are left in the Scipion working
>> directory.  I'm told that previously processed data will be deleted when a
>> new user starts collecting and starts a new Scipion run.
>>
>> The "Protocols SPA" view has a section titled "Export", but it doesn't
>> appear to list any plugins.
>>
>> Is my understanding correct?  How should we proceed?
>>
>> Matt
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] How to export files?

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

Hello Matt,

Thank you for your interest! At the moment there are two protocols (relion
- export ctf and relion - export particles) that can create a star file for
importing into Relion. You can find them by using Ctrl+F, it's true they
are not in export section at the moment (to be fixed).
If you also want to move the data files outside the project you will have
to fix the produced star file (awk can do it neatly).

The processed data is kept unless you overwrite/delete the project. Unless,
of course, if you plan to remove the old scipion projects as soon as the
session if finished.

Hope this helps,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542 <+44%201223%20267542>
e-mail: gs...@mr...


On Fri, May 24, 2019 at 4:24 PM Matt Harrington <ma...@ms...> wrote:

>
> We're evaluating Scipion for use by our facility, not necessarily for use
> by individual users.  I recently had a demo and was left with one
> question.  It's not clear how to export processed data to final
> destination.  We have a simple pipeline of Import -> MotionCor2 ->
> Ctffind.  It appears that processed files are left in the Scipion working
> directory.  I'm told that previously processed data will be deleted when a
> new user starts collecting and starts a new Scipion run.
>
> The "Protocols SPA" view has a section titled "Export", but it doesn't
> appear to list any plugins.
>
> Is my understanding correct?  How should we proceed?
>
> Matt
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] How to export files?

[Matt H. <ma...@ms...>]

We're evaluating Scipion for use by our facility, not necessarily for use
by individual users.  I recently had a demo and was left with one
question.  It's not clear how to export processed data to final
destination.  We have a simple pipeline of Import -> MotionCor2 ->
Ctffind.  It appears that processed files are left in the Scipion working
directory.  I'm told that previously processed data will be deleted when a
new user starts collecting and starts a new Scipion run.

The "Protocols SPA" view has a section titled "Export", but it doesn't
appear to list any plugins.

Is my understanding correct?  How should we proceed?

Matt

[scipion-users] OpenCV not found for Xmipp

[Hoover, D. (NIH/C. [E] <hoo...@hp...>]

Hi,

I recently installed Scipion 2.0 and all the plugins, and attempted to run the tutorials.  We have OpenCV installed in an alternate location, and I make it available by setting $PATH and $LD_LIBRARY_PATH.  I keep getting complaints that it is not installed, and that I should fix this and reinstall Xmipp.

How does Xmipp know where OpenCV is?  Can I set a configuration somewhere stating where it is located?

David Hoover
HPC @ NIH

[scipion-users] And xmipp too

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

Dear all,

I also take this mail to announce the release of Xmipp 19.04. It's 
release notes are in https://github.com/I2PC/xmipp/wiki/Release-notes 
and this new version contains many new algorithms like stream processing 
up to 3D reconstruction and estimation of 3D heterogeneity, MotionCorrB 
(a  very fast movie alignment using B-splines that generalizes 
MotionCorr2 and our Optical Flow), deep consensus (an algorithm to merge 
the output of multiple particle pickers and save 2D classification 
time), swarm consensus (an algorithm that automatically constructs 
initial volumes based on proposals by other algorithms), initial volume 
validation using SAXS experiments, highres (3D reconstruction of 
homogeneous populations), angular consensus (an algorithm to compare the 
angular assignment by two different algorithms),  heterogeneity 
metaprotocol (3D classification) allowing detailed control of the 
intermediate steps, many resolution algorithms measuring the resolution 
locally, directionally and in tomograms (MonoRes, MonoDir and MonoTomo), 
and localDeblur (an algorithm to sharpen maps that uses the local 
resolution information).

A short presentation with some of these results can be seen at

https://drive.google.com/file/d/1r3RnOw8pkp-BH5KvCxvAdoe-HUPtCddo/view?usp=sharing

[scipion-users] Scipion 2.0 is out

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

You might be aware of this, just in case not:

**

*Dear all,*

*

We are pleased to announce the new major release of version SCIPION 2.0 
<http://scipion.i2pc.es>. It is freely available for download on Linux here:


http://scipion.i2pc.es/download_form


Key changes for version 2.0 are:


  *

    Almost all existing EM packages were updated, such as RELION3,
    EMAN2.21, Gctf 1.18, SPIDER 25.02, Motioncor2-1.2.1 and others.


  *

    Model building tools from CCP4, Chimera, Phenix and powerfit have
    been added.


  *

    Several improvements for streaming: multi-GPU jobs distribution,
    more protocols supporting batch processing, jobs scheduling, new
    XMIPP streaming protocols (movie maxshift, ctf selection, GL2D
    classification on GPU etc.)


  *

    Multiple workflow usability and GUI improvements as well as bug
    fixes for several tasks.

**

  *

    Pluginization: each EM package is now a plugin developed and updated
    independently from Scipion core. This is a first step towards making
    Scipion even more modular and easy to use and install for both users
    and developers. The new repository hosting official plugins is now here:


https://github.com/scipion-em


For your convenience we have developed a Plugin Manager which provides 
an easy GUI to manage plugins and associated binaries. We already have 
over 30 plugins including several new ones, such as 3DFSC, CryoEF, 
Sphire (crYOLO), EMPIAR depositor and others. For more information on 
each plugin consult its corresponding repo and/ or developers.


  *

    For developers and facility managers we now have a slack workspace
    where you can easily reach other developers and facility staff to
    get a quick feedback: https://scipion.slack.com/. Contact us at
    sc...@cn... <mailto:sc...@cn...>for an invitation.


Installation instructions, pre-requisites and a full list of changes 
<https://scipion-em.github.io/docs/docs/developer/release-notes.html?highlight=release#v2-0-2019-05-16-diocletian> 
are available on our new documentation website 
<https://scipion-em.github.io/docs/>.


Best wishes,

Scipion team <http://scipion.i2pc.es/#whoweare>

*

Re: [scipion-users] Echoo..! 1 question survey...

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

Hi Matt! thanks, it is interesting indeed!

On 13/5/19 23:07, Matt Harrington wrote:
> On Tue, May 7, 2019 at 5:00 AM Pablo Conesa <pc...@cn...> wrote:
>
>> Which linux distro are you using to run Scipion?
> SBGrid provides free accounts for developers and free use of their
> build servers.  I highly recommend this.  More:
>
> https://sbgrid.org/computing/resources-for-developers/
>
> Matt
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Echoo..! 1 question survey...

[Matt H. <ma...@ms...>]

On Tue, May 7, 2019 at 5:00 AM Pablo Conesa <pc...@cn...> wrote:

> Which linux distro are you using to run Scipion?

SBGrid provides free accounts for developers and free use of their
build servers.  I highly recommend this.  More:

https://sbgrid.org/computing/resources-for-developers/

Matt

Re: [scipion-users] Echoo..! 1 question survey...

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

Can we make it up to 50!!!

Thank you all that reply (23). Feedback is important for us.  So far 
this is what is been collected.




Believe me, it is just 1 question, if your option is there you don't 
even need to type!

[scipion-users] Echoo..! 1 question survey...

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

Hi! It's been a long time, and actually not sure who is reading this list.

This will be a nice test!

We are about to release a new version of Scipion (shhh!): version 2.0.

To test the installation we want to focus our test on the most used 
Linux distro.

This is where your feedback is crucial:

Which linux distro are you using to run Scipion? 
<https://forms.gle/JFJBeDgo8nEpPpfw7>

[scipion-users] Faculty equivalent cryoEM position

[Hasan, S. S. <Ss...@so...>]

**************************************************************************************************

                        Faculty-Equivalent, Cryo-Electron Microscopy (Cryo-EM)



Position Summary:

As part of its program focused on advancing new measurement technologies and standards for biomolecular structure and function, the National Institute for Standards and Technology (NIST) Biomolecular Structure & Function Group seeks a ‘faculty-equivalent’ principle investigator to establish a research program focused on applications of cryo-electron microscopy (cryo-EM) in structural biology.  We are particularly interested in candidates with a focus on developing cryo-EM experimental techniques and data analysis tools, and who would leverage other structure methods [e.g. nuclear magnetic resonance (NMR), macromolecular crystallography and/or small angle scattering], to advance the current state-of-the-art in structure-function analysis of biological systems of biopharmaceutical interest.



The successful candidate should have a PhD or equivalent, a strong research portfolio and publication record that demonstrates evidence of cryo-EM expertise complementary to current group research strengths in NMR, crystallography and small angle scattering.  He/she is expected to become a recognized leader in the field of cryo-EM and contribute to collaborative projects both within the group and with external partners.  US Citizenship is required.



The Biomolecular Structure & Function Group is located at the Institute for Bioscience and Biotechnology Research (IBBR<http://www.ibbr.umd.edu/>), a joint federal-state research partnership between NIST and the University of Maryland.  IBBR operates state-of-the-art research facilities and is located in the heart of the biotechnology corridor in Rockville, Maryland. The Biomolecular Structure & Function Group is affiliated with the NIST Center for Neutron Research (NCNR<https://www.nist.gov/ncnr>) and the NIST Biomanufacturing<https://www.nist.gov/programs-projects/biomanufacturing-initiative> program. Our cryo-EM facility located at IBBR includes a newly installed 200 kV Talos-Arctica equipped with a Falcon III direct electron detector. A K3 direct electron detector and a Volta phase plate will be acquired soon in addition to a 200 kV Glacios microscope. State-of-the-art computational resources are available through the IBBR High Performance Computing Cluster.



Salary: Commensurate with qualifications.



Applications: Applicants should send cover letter, curriculum vitae, research statement, and contact information of three references to the attention of John P. Marino, Leader, Biomolecular Structure & Function Group: joh...@ni....

**************************************************************************************************

S. Saif Hasan, PhD


Assistant Professor

Department of Biochemistry and Molecular Biology

University of Maryland School of Medicine

108 N. Greene St., Baltimore, MD 21201


Group Leader

Center for Biomolecular Therapeutics (CBT)

Institute for Bioscience and Biotechnology Research (IBBR)

9600 Gudelsky Drive, Rockville, MD 20850

Phone: 240-314-6396

https://www.ibbr.umd.edu/profiles/s-saif-hasan

Re: [scipion-users] relion 3

[Elad B. <ela...@va...>]

Hi,
We use FOCUS in our facility to do all the preprocess on-the fly
(motioncor2 ,ctf) and the current version are able to export the dataset
for Relion3 processing.

Best,

On Fri, Feb 22, 2019 at 6:14 PM Jonathan Remis <re...@gm...> wrote:

> Hello Jose Miguel,
>
> We also have interest in using Relion3 from within Scipion.
>
> We currently are trying to use Scipion at our EM facility to monitor data
> as it is collected and typically use Motioncor2 to do the motion
> correction.   Many users want to use Relion3 to do their single particle
> reconstructions but because you are not able to import Motioncor2 fixed
> micrographs into Relion3 they need to re-run motion correction from within
> Relion3.  It would be ideal if we could give them motion corrected
> micrographs that they could directly use in the image processing program of
> their choice.    I was curious if Scipion will or does include access to
> this different multi-core cpu motion correction program?   I don't see it
> in the protocols after following the instructions you have posted in the
> link above.
>
> Thank you for your time-
>
> Jonathan_Remis
>
>
>
>
> On Thu, Feb 21, 2019 at 11:22 AM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Hi Daniel,
>>
>> I have updated the protocols in Scipion for support for Relion3. It is
>> beta right now,
>> but it has been used here in Stockholm and also a bit in Madrid. We
>> haven't announced
>> yet because we will wait until the next Scipion release (2.0) for that.
>>
>> I wrote some instructions to use it from the current Scipion version
>> (v1.2.1)
>> https://github.com/delarosatrevin/scipion/wiki/Testing-Relion-3-in-Scipion
>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__github.com_delarosatrevin_scipion_wiki_Testing-2DRelion-2D3-2Din-2DScipion%26d%3DDwMFaQ%26c%3DyHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws%26r%3DD_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs%26m%3DWyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8%26s%3DCRCn6MzQcPw3qmitElhcn8pmM9Kl0tOeUkMbYMZ3j1Y%26e%3D&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C0d238b15b65b44df39d108d699241cca%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636864777724240833&sdata=kDJA72Yvj7CV9fW1M%2B0oaGmFNVJcZfR423T1DmvTiHY%3D&reserved=0>
>>
>> Please don't hesitate to contact me if you need some help to update the
>> Scipion
>> installation for Relion 3 support.
>>
>> Cheers,
>> Jose Miguel
>>
>>
>> On Thu, Feb 21, 2019 at 8:15 PM Daniel Larsson <dan...@ic...>
>> wrote:
>>
>>> When can we expect to have Relion 3 in Scipion?
>>>
>>> Regards,
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> När du har kontakt med oss på Uppsala universitet med e-post så innebär
>>> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
>>> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.uu.se_om-2Duu_dataskydd-2Dpersonuppgifter_%26d%3DDwMFaQ%26c%3DyHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws%26r%3DD_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs%26m%3DWyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8%26s%3Ddkikw7mjMEXQv49mvuBwlxb1cJkVXRxG3AmbkunfG2M%26e%3D&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C0d238b15b65b44df39d108d699241cca%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636864777724250838&sdata=1Kv4n9v%2B8dpB8tkSlNsqyttDBjbp8ceP621cu6pNHvQ%3D&reserved=0>
>>>
>>> E-mailing Uppsala University means that we will process your personal
>>> data. For more information on how this is performed, please read here:
>>> http://www.uu.se/en/about-uu/data-protection-policy
>>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.uu.se_en_about-2Duu_data-2Dprotection-2Dpolicy%26d%3DDwMFaQ%26c%3DyHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws%26r%3DD_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs%26m%3DWyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8%26s%3DRK_UWtpA0f17OqJcNEoOhgHlx17xuQebeNLAgyTQTJo%26e%3D&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C0d238b15b65b44df39d108d699241cca%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636864777724250838&sdata=2ZpFBlWCqPPeBlsy8X0EXoaPdSe%2Bs6zj0T1t5YSikEk%3D&reserved=0>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers%26d%3DDwMFaQ%26c%3DyHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws%26r%3DD_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs%26m%3DWyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8%26s%3DssmbZPXx-h2A2Dui30QXYhFos9EnjGtqbGt4t73G0T8%26e%3D&data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C0d238b15b65b44df39d108d699241cca%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636864777724260848&sdata=p%2Bj4Hiyzzq8nH32GTXOyy6kdwqhobL4ataVmQgxM%2FI8%3D&reserved=0>
>>>
>> _______________________________________________
> scipion-users mailing list
> sci...@li...
>
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&amp;data=02%7C01%7Celad.binshtein%40vanderbilt.edu%7C0d238b15b65b44df39d108d699241cca%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636864777724270857&amp;sdata=JL%2Fnu%2FFdHc%2FrVcg%2B7mrUnm6hPVDSCwl9JhcQIv3gDEo%3D&amp;reserved=0
>


-- 
________________________________
Elad Binshtein, Ph.D.
Cryo-EM specialist - Senior Staff Scientist
Center for Structure Biology (CSB)
MCN Room 1207
Vanderbilt University
Nashville, TN
Office: +1-615-322-4671
Mobile: +1-615-481-4408
https://www.linkedin.com/in/elad-binshtein-6bb89428/
E-Mail: ela...@va... <el...@gm...>
twitter @EladBinshtein
________________________________

Re: [scipion-users] relion 3

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

Hi Jonathan,

That's great! Please use the current implementation in my branch while we
are in the process of the new release. We will be very happy to help you
with any problem or take into account your feedback.

The Relion's implementation of motion correction is available in Scipion in
that branch. Within Scipion, you could use it, or motioncor2 or any
global/local alignment method and later combine with the Relion's Bayesian
Polishing, since we take care of the proper generation of the required star
files. In our facility here in Stockholm, we routinely go until 2D
classification and in some cases to initial 3D volume and refinement. Some
of our users also want to take their pre-processed data and go to Relion or
CryoSparc, so I have implemented a couple protocols that are quite useful
for that: "relion - export ctf" and "relion - export particles" .

Regarding the protocols that does not appear...you can always try Ctrl + F
to open the Search Protocol Dialog and check if they appear there. It is
probably due to the old protocols.conf that does not contains the new
protocol. You could remove it and generate again (from the scipion folder):
rm config/protocols.conf
./scipion config

Hope this helps,
Best,
Jose Miguel


On Sat, Feb 23, 2019 at 1:16 AM Jonathan Remis <re...@gm...> wrote:

> Hello Jose Miguel,
>
> We also have interest in using Relion3 from within Scipion.
>
> We currently are trying to use Scipion at our EM facility to monitor data
> as it is collected and typically use Motioncor2 to do the motion
> correction.   Many users want to use Relion3 to do their single particle
> reconstructions but because you are not able to import Motioncor2 fixed
> micrographs into Relion3 they need to re-run motion correction from within
> Relion3.  It would be ideal if we could give them motion corrected
> micrographs that they could directly use in the image processing program of
> their choice.    I was curious if Scipion will or does include access to
> this different multi-core cpu motion correction program?   I don't see it
> in the protocols after following the instructions you have posted in the
> link above.
>
> Thank you for your time-
>
> Jonathan_Remis
>
>
>
>
> On Thu, Feb 21, 2019 at 11:22 AM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Hi Daniel,
>>
>> I have updated the protocols in Scipion for support for Relion3. It is
>> beta right now,
>> but it has been used here in Stockholm and also a bit in Madrid. We
>> haven't announced
>> yet because we will wait until the next Scipion release (2.0) for that.
>>
>> I wrote some instructions to use it from the current Scipion version
>> (v1.2.1)
>> https://github.com/delarosatrevin/scipion/wiki/Testing-Relion-3-in-Scipion
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_delarosatrevin_scipion_wiki_Testing-2DRelion-2D3-2Din-2DScipion&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=CRCn6MzQcPw3qmitElhcn8pmM9Kl0tOeUkMbYMZ3j1Y&e=>
>>
>> Please don't hesitate to contact me if you need some help to update the
>> Scipion
>> installation for Relion 3 support.
>>
>> Cheers,
>> Jose Miguel
>>
>>
>> On Thu, Feb 21, 2019 at 8:15 PM Daniel Larsson <dan...@ic...>
>> wrote:
>>
>>> When can we expect to have Relion 3 in Scipion?
>>>
>>> Regards,
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> När du har kontakt med oss på Uppsala universitet med e-post så innebär
>>> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
>>> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_om-2Duu_dataskydd-2Dpersonuppgifter_&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=dkikw7mjMEXQv49mvuBwlxb1cJkVXRxG3AmbkunfG2M&e=>
>>>
>>> E-mailing Uppsala University means that we will process your personal
>>> data. For more information on how this is performed, please read here:
>>> http://www.uu.se/en/about-uu/data-protection-policy
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_en_about-2Duu_data-2Dprotection-2Dpolicy&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=RK_UWtpA0f17OqJcNEoOhgHlx17xuQebeNLAgyTQTJo&e=>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=ssmbZPXx-h2A2Dui30QXYhFos9EnjGtqbGt4t73G0T8&e=>
>>>
>> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] relion 3

[Jonathan R. <re...@gm...>]

Hello Jose Miguel,

We also have interest in using Relion3 from within Scipion.

We currently are trying to use Scipion at our EM facility to monitor data
as it is collected and typically use Motioncor2 to do the motion
correction.   Many users want to use Relion3 to do their single particle
reconstructions but because you are not able to import Motioncor2 fixed
micrographs into Relion3 they need to re-run motion correction from within
Relion3.  It would be ideal if we could give them motion corrected
micrographs that they could directly use in the image processing program of
their choice.    I was curious if Scipion will or does include access to
this different multi-core cpu motion correction program?   I don't see it
in the protocols after following the instructions you have posted in the
link above.

Thank you for your time-

Jonathan_Remis




On Thu, Feb 21, 2019 at 11:22 AM Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Hi Daniel,
>
> I have updated the protocols in Scipion for support for Relion3. It is
> beta right now,
> but it has been used here in Stockholm and also a bit in Madrid. We
> haven't announced
> yet because we will wait until the next Scipion release (2.0) for that.
>
> I wrote some instructions to use it from the current Scipion version
> (v1.2.1)
> https://github.com/delarosatrevin/scipion/wiki/Testing-Relion-3-in-Scipion
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_delarosatrevin_scipion_wiki_Testing-2DRelion-2D3-2Din-2DScipion&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=CRCn6MzQcPw3qmitElhcn8pmM9Kl0tOeUkMbYMZ3j1Y&e=>
>
> Please don't hesitate to contact me if you need some help to update the
> Scipion
> installation for Relion 3 support.
>
> Cheers,
> Jose Miguel
>
>
> On Thu, Feb 21, 2019 at 8:15 PM Daniel Larsson <dan...@ic...>
> wrote:
>
>> When can we expect to have Relion 3 in Scipion?
>>
>> Regards,
>> Daniel
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> När du har kontakt med oss på Uppsala universitet med e-post så innebär
>> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
>> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_om-2Duu_dataskydd-2Dpersonuppgifter_&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=dkikw7mjMEXQv49mvuBwlxb1cJkVXRxG3AmbkunfG2M&e=>
>>
>> E-mailing Uppsala University means that we will process your personal
>> data. For more information on how this is performed, please read here:
>> http://www.uu.se/en/about-uu/data-protection-policy
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_en_about-2Duu_data-2Dprotection-2Dpolicy&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=RK_UWtpA0f17OqJcNEoOhgHlx17xuQebeNLAgyTQTJo&e=>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_scipion-2Dusers&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=ssmbZPXx-h2A2Dui30QXYhFos9EnjGtqbGt4t73G0T8&e=>
>>
>

Re: [scipion-users] relion 3

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

Hi Daniel,

I have updated the protocols in Scipion for support for Relion3. It is beta
right now,
but it has been used here in Stockholm and also a bit in Madrid. We haven't
announced
yet because we will wait until the next Scipion release (2.0) for that.

I wrote some instructions to use it from the current Scipion version
(v1.2.1)
https://github.com/delarosatrevin/scipion/wiki/Testing-Relion-3-in-Scipion

Please don't hesitate to contact me if you need some help to update the
Scipion
installation for Relion 3 support.

Cheers,
Jose Miguel


On Thu, Feb 21, 2019 at 8:15 PM Daniel Larsson <dan...@ic...>
wrote:

> When can we expect to have Relion 3 in Scipion?
>
> Regards,
> Daniel
>
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] relion 3

[Daniel L. <dan...@ic...>]

When can we expect to have Relion 3 in Scipion?

Regards,
Daniel









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

[scipion-users] Fwd: relion_localized_reconstruction - weird results

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

I do not think this made it to the list.

I'm forwarding it on behalf of Stefano.



-------- Forwarded Message --------
Subject: 	relion_localized_reconstruction - weird results
Date: 	Wed, 23 Jan 2019 16:06:37 +0100
From: 	Stefano Trapani <tr...@cb...>
Organisation: 	Centre de Biochimie Structurale
To: 	sci...@li..., CCPEM <CC...@JI...>



Dear all

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

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

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

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

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

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

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

Best regards

-- 
Stefano Trapani

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

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