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From: Jose M. de la R. T. <del...@gm...> - 2017-03-21 09:56:19
|
Hi Kevin,
You can delete it...I usually do (after I'm sure the installation is
finished and working properly):
rm -rf scipion/software/tmp/*
I will update the "How to install" wiki page..because I think it is an
important action to do for clean up the installation and saving disk space.
Cheers,
Jose MIguel.
On Tue, Mar 21, 2017 at 10:45 AM, <kev...@di...> wrote:
> Hi All,
>
> Just a quick question about the directory {scipion}/software/tmp. Can I
> safely delete the contents of this directory once the install is complete?
>
> Thanks,
> Kevin
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> ------------------------------------------------------------
> ------------------
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> _______________________________________________
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> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: <kev...@di...> - 2017-03-21 09:45:52
|
Hi All,
Just a quick question about the directory {scipion}/software/tmp. Can I safely delete the contents of this directory once the install is complete?
Thanks,
Kevin
--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
|
|
From: Jose M. de la R. T. <del...@gm...> - 2017-03-20 12:15:08
|
Wolfgang, thanks a lot for your feedback!!! On Mon, Mar 20, 2017 at 1:10 PM, Wolfgang Lugmayr <w.l...@uk...> wrote: > hi, > > i just compiled and installed it for small tests, since my laptop is too > weak to run huge analysis. > > you need the openjdk-7-jdk package instead of 8. the rest runs as on the > install page without any further problems. > this is not a full ubuntu, since it lacks the linux kernel. its a > bash/ubuntu subsystem. > so you cannot use the gpu, because you cannot load the nvidia kernel > module. > but most packages work there anyway and you can use the normal ubuntu > repository. > cryosparc is not working due the lack of gpu support in the subsystem. > > you cannot start a whole gnome/kde session (they need dbus which does not > exist), but you can start individual gnome/kde programs with the external > x-server on windows. > > but if you use e.g. chimerax on windows directly (gpu support) and > calculate on the ubuntu subsystem with linux programs, its fine to use. the > ubuntu subsystem can access all local files from windows 10 (/mnt/c etc.). > from windows you can call most ubuntu programs via bash.exe -c scriptname. > > nfs mounts of remote fileservers is not supported, so you would need your > data on a usb3 drive (e.g. /mnt/d). > > cheers, > wolfgang > > > > Am 20.03.2017 um 11:12 schrieb Jose Miguel de la Rosa Trevin: > > Thanks Wolfgang...Have you used Scipion in Windows 10 through the Ubuntu > bash console? If so I would be interested in hear about your experience. > > Dmitry, we haven't tried it ourselves...you always have the option to > install a virtual machine through VirtualBox. > > Cheers, > Jose Miguel. > > > On Mon, Mar 20, 2017 at 11:05 AM, Wolfgang Lugmayr <w.l...@uk...> > wrote: > >> hi dimitry, >> >> to run the scipion gui on bash on windows on ubuntu you need an x-server >> to display the gui (same for the relion gui): >> https://sourceforge.net/projects/vcxsrv/ >> >> cheers, >> wolfgang >> >> >> >> On 03/20/2017 10:16 AM, Dmitry Semchonok wrote: >> >> Dear colleagues, >> >> It seems that the time has come for me to try installation of the Scipion >> myself on the home machine. Initially I have Windows 10 on it. >> >> What linux operation system could you recommend? As I understand Windows >> is not yet supported? >> >> Yesterday I tried to install bash Ubuntu on windows 10 but I'm not sure >> if the futher installation of the Scipion will go smoothly. >> >> >> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> -- >> Universitätsklinikum Hamburg-Eppendorf (UKE) >> @ Centre for Structral Systems Biology (CSSB) >> @ Institute of Molecular Biotechnology (IMBA) >> Dr. Bohr-Gasse 3-7 (Room 6.14) >> 1030 Vienna, Austria >> Tel.: +43 (1) 790 44-4649 <+43%201%20790444649> >> Email: w.l...@uk...http://www.cssb-hamburg.de/ >> >> ------------------------------ >> >> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen >> Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. >> Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim >> Prölß, Rainer Schoppik >> ------------------------------ >> >> SAVE PAPER - THINK BEFORE PRINTING >> ------------------------------------------------------------------------------ >> 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 > > > ------------------------------ > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen > Rechts; Gerichtsstand: Hamburg | www.uke.de > Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. > Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik > ------------------------------ > > SAVE PAPER - THINK BEFORE PRINTING > |
|
From: Wolfgang L. <w.l...@uk...> - 2017-03-20 12:11:19
|
hi, i just compiled and installed it for small tests, since my laptop is too weak to run huge analysis. you need the openjdk-7-jdk package instead of 8. the rest runs as on the install page without any further problems. this is not a full ubuntu, since it lacks the linux kernel. its a bash/ubuntu subsystem. so you cannot use the gpu, because you cannot load the nvidia kernel module. but most packages work there anyway and you can use the normal ubuntu repository. cryosparc is not working due the lack of gpu support in the subsystem. you cannot start a whole gnome/kde session (they need dbus which does not exist), but you can start individual gnome/kde programs with the external x-server on windows. but if you use e.g. chimerax on windows directly (gpu support) and calculate on the ubuntu subsystem with linux programs, its fine to use. the ubuntu subsystem can access all local files from windows 10 (/mnt/c etc.). from windows you can call most ubuntu programs via bash.exe -c scriptname. nfs mounts of remote fileservers is not supported, so you would need your data on a usb3 drive (e.g. /mnt/d). cheers, wolfgang Am 20.03.2017 um 11:12 schrieb Jose Miguel de la Rosa Trevin: > Thanks Wolfgang...Have you used Scipion in Windows 10 through the > Ubuntu bash console? If so I would be interested in hear about your > experience. > > Dmitry, we haven't tried it ourselves...you always have the option to > install a virtual machine through VirtualBox. > > Cheers, > Jose Miguel. > > > On Mon, Mar 20, 2017 at 11:05 AM, Wolfgang Lugmayr <w.l...@uk... > <mailto:w.l...@uk...>> wrote: > > hi dimitry, > > to run the scipion gui on bash on windows on ubuntu you need an > x-server to display the gui (same for the relion gui): > https://sourceforge.net/projects/vcxsrv/ > <https://sourceforge.net/projects/vcxsrv/> > > cheers, > wolfgang > > > > On 03/20/2017 10:16 AM, Dmitry Semchonok wrote: >> Dear colleagues, >> >> It seems that the time has come for me to try installation of the >> Scipion myself on the home machine. Initially I have Windows 10 >> on it. >> >> What linux operation system could you recommend? As I understand >> Windows is not yet supported? >> >> Yesterday I tried to install bash Ubuntu on windows 10 but I'm >> not sure if the futher installation of the Scipion will go smoothly. >> >> >> 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... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Institute of Molecular Biotechnology (IMBA) > Dr. Bohr-Gasse 3-7 (Room 6.14) > 1030 Vienna, Austria > Tel.:+43 (1) 790 44-4649 <tel:+43%201%20790444649> > Email:w.l...@uk... <mailto:w.l...@uk...> > http://www.cssb-hamburg.de/ > > ------------------------------------------------------------------------ > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des > öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de > <http://www.uke.de> Vorstandsmitglieder: Prof. Dr. Burkhard Göke > (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, > Rainer Schoppik > > ------------------------------------------------------------------------ > > SAVE PAPER - THINK BEFORE PRINTING > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ scipion-users > mailing list sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-03-20 10:12:12
|
Thanks Wolfgang...Have you used Scipion in Windows 10 through the Ubuntu bash console? If so I would be interested in hear about your experience. Dmitry, we haven't tried it ourselves...you always have the option to install a virtual machine through VirtualBox. Cheers, Jose Miguel. On Mon, Mar 20, 2017 at 11:05 AM, Wolfgang Lugmayr <w.l...@uk...> wrote: > hi dimitry, > > to run the scipion gui on bash on windows on ubuntu you need an x-server > to display the gui (same for the relion gui): > https://sourceforge.net/projects/vcxsrv/ > > cheers, > wolfgang > > > > On 03/20/2017 10:16 AM, Dmitry Semchonok wrote: > > Dear colleagues, > > It seems that the time has come for me to try installation of the Scipion > myself on the home machine. Initially I have Windows 10 on it. > > What linux operation system could you recommend? As I understand Windows > is not yet supported? > > Yesterday I tried to install bash Ubuntu on windows 10 but I'm not sure if > the futher installation of the Scipion will go smoothly. > > > 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > -- > Universitätsklinikum Hamburg-Eppendorf (UKE) > @ Centre for Structral Systems Biology (CSSB) > @ Institute of Molecular Biotechnology (IMBA) > Dr. Bohr-Gasse 3-7 (Room 6.14) > 1030 Vienna, Austria > Tel.: +43 (1) 790 44-4649 <+43%201%20790444649> > Email: w.l...@uk...http://www.cssb-hamburg.de/ > > > ------------------------------ > > Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen > Rechts; Gerichtsstand: Hamburg | www.uke.de > Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. > Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik > ------------------------------ > > SAVE PAPER - THINK BEFORE PRINTING > > ------------------------------------------------------------ > ------------------ > 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 > > |
|
From: Wolfgang L. <w.l...@uk...> - 2017-03-20 10:05:48
|
hi dimitry, to run the scipion gui on bash on windows on ubuntu you need an x-server to display the gui (same for the relion gui): https://sourceforge.net/projects/vcxsrv/ cheers, wolfgang On 03/20/2017 10:16 AM, Dmitry Semchonok wrote: > Dear colleagues, > > It seems that the time has come for me to try installation of the > Scipion myself on the home machine. Initially I have Windows 10 on it. > > What linux operation system could you recommend? As I understand > Windows is not yet supported? > > Yesterday I tried to install bash Ubuntu on windows 10 but I'm not > sure if the futher installation of the Scipion will go smoothly. > > > 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 -- Universitätsklinikum Hamburg-Eppendorf (UKE) @ Centre for Structral Systems Biology (CSSB) @ Institute of Molecular Biotechnology (IMBA) Dr. Bohr-Gasse 3-7 (Room 6.14) 1030 Vienna, Austria Tel.: +43 (1) 790 44-4649 Email: w.l...@uk... http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING |
|
From: Dmitry S. <sem...@gm...> - 2017-03-20 09:17:01
|
Dear colleagues, It seems that the time has come for me to try installation of the Scipion myself on the home machine. Initially I have Windows 10 on it. What linux operation system could you recommend? As I understand Windows is not yet supported? Yesterday I tried to install bash Ubuntu on windows 10 but I'm not sure if the futher installation of the Scipion will go smoothly. Sincerely, Dmitry |
|
From: Dmitry A. S. <sem...@gm...> - 2017-03-10 14:33:21
|
Thank you! Sincerely, Dmitry Dear Dmitry, in Scipion, hot-pixels are normally removed when particles are extracted. In the preprocess tab there is an option called dust removal. Kind regards, Carlos Oscar Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/68 Activo Vie, 10 Marzo at 1:25 PM , Dmitry Semchonok <sem...@gm...> Escrito: Dear colleagues, I have question about the hot pixels. How to fix the presence of hot pixels on the different levels - movie stacks, picked particles? And what is an ordinary procedure to fix the hot pixels? Sincerely, Dmitry ------------------------------------------------------------------------------ Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Dmitry A. S. <sem...@gm...> - 2017-03-10 14:32:31
|
Dear Pablo,
I'm now at the particle picking stage.
We applied the fix for that updates of the protocols in the SCIPION 1.1.
The problem still remains - some particles i can not delete pressing
shift+left mouse button. But i noticed that if i use only the eraser tool
then i can delete all the selections.
Sincerely,
Dmitry
Hi Dmitry, did this worked?
All the best, Pablo.
Scipion team
Activo Mar, 7 Marzo at 10:42 AM
, Pablo Conesa <su...@bc...> Escrito:
Hi Dmitry, May I recomend you to switch to release-1.1 branch. Reasons are:
Now devel and release-1.1 are almost similar. Differences are that release
has more activity and bugfixes are pushed first to release-1.1 and after a
while they end up un devel. Like in this case for the picking bug that is
not yet in devel but soon will be.
You will also help us to test the future release while using it.
To do so, follow Jose Miguel steps but switch to release-1.1:
git pull # and this should bring the changes...and release-1.1 branch if
not yet local.
git checkout release-1.1 #This switches you to release-1.1 branch
git pull # Again, this might not be needed, but I use to do it to be sure I
have the latest changes.
scipion install -j N # replace N by an integer, it means how many CPUs you
want to use to compile
scipion install is optimized and will only compile what has changed and EM
packages are not reinstall. It should not take long.
Let us know how it goes?
All the best, Pablo.
Activo Lun, 6 Marzo at 5:08 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues, If there an easy way to update the xmipp -
particle picking protocol in Scipion_dev (or any other protocol inside
Scipion dev that was bug fixed) without reinstalling everything?
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
|
|
From: Pablo C. <su...@bc...> - 2017-03-10 14:15:27
|
Hi Dmitry, did this worked?
All the best, Pablo.
Scipion team
Activo Mar, 7 Marzo at 10:42 AM
, Pablo Conesa <su...@bc...> Escrito:
Hi Dmitry, May I recomend you to switch to release-1.1 branch. Reasons are:
Now devel and release-1.1 are almost similar. Differences are that release has more activity and bugfixes are pushed first to release-1.1 and after a while they end up un devel. Like in this case for the picking bug that is not yet in devel but soon will be.
You will also help us to test the future release while using it.
To do so, follow Jose Miguel steps but switch to release-1.1:
git pull # and this should bring the changes...and release-1.1 branch if not yet local.
git checkout release-1.1 #This switches you to release-1.1 branch
git pull # Again, this might not be needed, but I use to do it to be sure I have the latest changes.
scipion install -j N # replace N by an integer, it means how many CPUs you want to use to compile
scipion install is optimized and will only compile what has changed and EM packages are not reinstall. It should not take long.
Let us know how it goes?
All the best, Pablo.
Activo Lun, 6 Marzo at 5:08 PM
, Dmitry Semchonok <sem...@gm...> Escrito:
Dear colleagues, If there an easy way to update the xmipp - particle picking protocol in Scipion_dev (or any other protocol inside Scipion dev that was bug fixed) without reinstalling everything? 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
|
|
From: Carlos O. S. <su...@bc...> - 2017-03-10 13:37:06
|
Dear Dmitry, in Scipion, hot-pixels are normally removed when particles are extracted. In the preprocess tab there is an option called dust removal. Kind regards, Carlos Oscar Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/68 Activo Vie, 10 Marzo at 1:25 PM , Dmitry Semchonok <sem...@gm...> Escrito: Dear colleagues, I have question about the hot pixels. How to fix the presence of hot pixels on the different levels - movie stacks, picked particles? And what is an ordinary procedure to fix the hot pixels? Sincerely, Dmitry ------------------------------------------------------------------------------ Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry A. S. <sem...@gm...> - 2017-03-10 12:25:26
|
Dear colleagues, I have question about the hot pixels. How to fix the presence of hot pixels on the different levels - movie stacks, picked particles? And what is an ordinary procedure to fix the hot pixels? Sincerely, Dmitry |
|
From: Pablo C. <su...@bc...> - 2017-03-10 09:11:59
|
Hi Simone
If you want to stay in the current release, then, my guess, is that , although it's a bug, you might be entering some "rare" combination of parameters
Could you please send us a screenshot of the "import movies" form where we can see the parameters populated?
All the best, Pablo.
Scipion team
Activo Vie, 10 Marzo at 7:47 AM
, Carlos Oscar Sorzano <su...@bc...> Escrito:
Hi Simone,
this sounds more like a code issue rather than a python one. We will have a look at it, but note that Release 1.1 is about to be released and most likely the quickest solution is already to change to this branch (if you have downloaded Scipion through git)
Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/66
Activo Jue, 9 Marzo at 7:54 PM
, Simone PELLEGRINO <pel...@ig...> Escrito:
Dear all,
I am experiencing a problem when running the movie extract particles in scipion v 1.0.1
The error I have is the following:
TypeError: processMovieStep() takes exactly 3 arguments (4 given)
Protocol failed: processMovieStep() takes exactly 3 arguments (4 given)
From a quick search on internet looks like a Python issue, does this relate with the version of Python or is it a code issue please?
Many thanks in advance
Best
Simone
Dr. Simone Pellegrino
Integrated Structural Biology
Marat Yusupov's team
I.G.B.M.C.
1, rue Laurent Fries
BP 10142 - 67404 Illkirch CEDEX
Tel: +33 (0)3 88 65 33 52
E.mail: sim...@ig...
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From: Carlos O. S. <su...@bc...> - 2017-03-10 06:48:06
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Hi Simone, this sounds more like a code issue rather than a python one. We will have a look at it, but note that Release 1.1 is about to be released and most likely the quickest solution is already to change to this branch (if you have downloaded Scipion through git) Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/66 Activo Jue, 9 Marzo at 7:54 PM , Simone PELLEGRINO <pel...@ig...> Escrito: Dear all, I am experiencing a problem when running the movie extract particles in scipion v 1.0.1 The error I have is the following: TypeError: processMovieStep() takes exactly 3 arguments (4 given) Protocol failed: processMovieStep() takes exactly 3 arguments (4 given) From a quick search on internet looks like a Python issue, does this relate with the version of Python or is it a code issue please? Many thanks in advance Best Simone Dr. Simone Pellegrino Integrated Structural Biology Marat Yusupov's team I.G.B.M.C. 1, rue Laurent Fries BP 10142 - 67404 Illkirch CEDEX Tel: +33 (0)3 88 65 33 52 E.mail: sim...@ig... |
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From: Simone P. <pel...@ig...> - 2017-03-09 18:54:42
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Dear all, I am experiencing a problem when running the movie extract particles in scipion v 1.0.1 The error I have is the following: TypeError: processMovieStep() takes exactly 3 arguments (4 given) Protocol failed: processMovieStep() takes exactly 3 arguments (4 given) >From a quick search on internet looks like a Python issue, does this relate with the version of Python or is it a code issue please? Many thanks in advance Best Simone ? Dr. Simone Pellegrino Integrated Structural Biology Marat Yusupov's team I.G.B.M.C. 1, rue Laurent Fries BP 10142 - 67404 Illkirch CEDEX Tel: +33 (0)3 88 65 33 52 E.mail: sim...@ig... |
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From: Simone P. <pel...@ig...> - 2017-03-09 16:22:13
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Dear all, I am experiencing a problem when running the movie extract particles in scipion v 1.0.1 The error I have is the following: TypeError: processMovieStep() takes exactly 3 arguments (4 given) Protocol failed: processMovieStep() takes exactly 3 arguments (4 given) Form a quick research on internet looks like a Python issue, does this relate with the version of Python or is it a code issue please? Many thanks in advance Best Simone Dr. Simone Pellegrino Integrated Structural Biology Marat Yusupov's team I.G.B.M.C. 1, rue Laurent Fries BP 10142 - 67404 Illkirch CEDEX Tel: +33 (0)3 88 65 33 52 E.mail: sim...@ig... |
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From: Jose M. de la R. T. <del...@gm...> - 2017-03-08 18:44:07
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Hi Juha, As Pablo said, Relion 2.0 helical processing will not be supported for the upcoming release, and there are other stuff pending in the roadmap. But I guess that many other people will find helpful to have that workflow inside Scipion, specially if requires to combine more than one package (EMAN2 and Relion in this case). I have not much experience (almost none) with helical processing, but it seems that you have a very clear workflow and idea about how it can be implemented in Scipion. I think that I could dedicate some time to get it done, but only if we manage to do it together. In this case will not take much time from both sides. If you are interested we can further discuss a concrete plan to go ahead. Kind regards, Jose Miguel On Wed, Mar 8, 2017 at 5:25 PM, Pablo Conesa <su...@bc...> wrote: > Dear Juha > > Supporting helix processing is part of our roadmap among tomography. > > To be honest we don't see it happen in the "near future" (less than 6 > months). > > > All the best, Pablo. > Scipion team > > Activo Mar, 7 Marzo at 7:34 PM , Juha Huiskonen <ju...@st...> > Escrito: > Hello Developers, > > I currently pick filaments with helical symmetry using helixboxer of EMAN2 > and save BOX files. Currently I process everything in Relion 2.0 using, but > would be nice to do everything from Scipion. Once Relion 2.0 becomes > available I guess we are one step closer. But I have a couple of questions > what your plans are: > > - will Scipion support helical processing through Relion? > - can filament coordinates be exported from BOX files? > - could e2helixboxer GUI be supported? in addition to e2boxer? > - will the in-plane angle retained from the filament end-points? > > Best wishes, > Juha > > 61 > > ------------------------------------------------------------ > ------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Pablo C. <su...@bc...> - 2017-03-08 16:25:40
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Dear Juha Supporting helix processing is part of our roadmap among tomography.
To be honest we don't see it happen in the "near future" (less than 6 months).
All the best, Pablo.
Scipion team
Activo Mar, 7 Marzo at 7:34 PM
, Juha Huiskonen <ju...@st...> Escrito:
Hello Developers,
I currently pick filaments with helical symmetry using helixboxer of EMAN2 and save BOX files. Currently I process everything in Relion 2.0 using, but would be nice to do everything from Scipion. Once Relion 2.0 becomes available I guess we are one step closer. But I have a couple of questions what your plans are:
- will Scipion support helical processing through Relion?
- can filament coordinates be exported from BOX files?
- could e2helixboxer GUI be supported? in addition to e2boxer?
- will the in-plane angle retained from the filament end-points?
Best wishes,
Juha
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From: Jose M. de la R. T. <del...@gm...> - 2017-03-08 14:36:04
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Hi Juha, The angular assignment information in a 3D classification and 3D refinement should be similar, with the main difference that the former could be associated to many classes. I will check this problem, because, as you expected, exporting on 3D class assigned particles should produce a volume similar to the class representative 3D structure. Please let us know about any news from CryoSparc developers regarding the EMX import. Bests, Jose Miguel. On Wed, Mar 8, 2017 at 3:28 PM, Juha Huiskonen <ju...@st...> wrote: > Hi Jose Miguel > > First I tried exporting a setOfParticles, saved from a 3D classification > (all particles from one class), to an EMX file. After importing back to > Scipion (choosing alignment type Projection), this produced a smooth blob. > Next I tried the same, but from a 3D refinement that I had run on the same > set of particles. This worked just fine. So is the alignment information > stored / exported somehow differently for setOfParticles object in these > two cases? > > CryoSparc was not working even now so I will ask the developers. > > Best wishes, > Juha > > On Sat, Mar 4, 2017 at 10:03 AM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Hi Juha, >> >> Thanks for your feedback. Could you do a small experiment to detect if >> the exported EMX file is correct? Could you import back the EMX file into >> Scipion and try to reconstruct only with Relion (there is a protocol for >> that) and check if it makes sense or not. Take into account that the map >> probably will not be exactly the same that originally came out from Relion, >> since it is filtered. >> >> Anyway we will also check about this issue. >> >> Bests, >> Jose Miguel >> >> >> On Fri, Mar 3, 2017 at 9:46 AM, Juha Huiskonen <ju...@st...> >> wrote: >> >>> Hello >>> >>> I was wondering if the EMX export should work and if others have managed >>> to use it with cryoSparc? >>> >>> I exported my dataset and imported EMX files to cryoSPARC after running >>> Relion 3D refinement through Scipion. Import to CryoSparc seemed to work >>> (it created a gallery of the images) but results from the first ab initio >>> run were nonsensical. >>> >>> Next I tested importing MRC files and a corresponding STAR file >>> (manually converting the same particle stacks to MRC and providing them >>> together with a corresponding Relion STAR file from the refinement run). >>> After the same run in cryoSparc, the results were as expected. >>> >>> Any ideas? Apologies if this is likely to be an issue on the cryoSPARC >>> side, in this case I would naturally contact those developers. >>> >>> Best wishes, >>> Juha >>> >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > |
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From: Juha H. <ju...@st...> - 2017-03-08 14:29:02
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Hi Jose Miguel First I tried exporting a setOfParticles, saved from a 3D classification (all particles from one class), to an EMX file. After importing back to Scipion (choosing alignment type Projection), this produced a smooth blob. Next I tried the same, but from a 3D refinement that I had run on the same set of particles. This worked just fine. So is the alignment information stored / exported somehow differently for setOfParticles object in these two cases? CryoSparc was not working even now so I will ask the developers. Best wishes, Juha On Sat, Mar 4, 2017 at 10:03 AM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hi Juha, > > Thanks for your feedback. Could you do a small experiment to detect if the > exported EMX file is correct? Could you import back the EMX file into > Scipion and try to reconstruct only with Relion (there is a protocol for > that) and check if it makes sense or not. Take into account that the map > probably will not be exactly the same that originally came out from Relion, > since it is filtered. > > Anyway we will also check about this issue. > > Bests, > Jose Miguel > > > On Fri, Mar 3, 2017 at 9:46 AM, Juha Huiskonen <ju...@st...> > wrote: > >> Hello >> >> I was wondering if the EMX export should work and if others have managed >> to use it with cryoSparc? >> >> I exported my dataset and imported EMX files to cryoSPARC after running >> Relion 3D refinement through Scipion. Import to CryoSparc seemed to work >> (it created a gallery of the images) but results from the first ab initio >> run were nonsensical. >> >> Next I tested importing MRC files and a corresponding STAR file (manually >> converting the same particle stacks to MRC and providing them together with >> a corresponding Relion STAR file from the refinement run). After the same >> run in cryoSparc, the results were as expected. >> >> Any ideas? Apologies if this is likely to be an issue on the cryoSPARC >> side, in this case I would naturally contact those developers. >> >> Best wishes, >> Juha >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
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From: Sergey N. <ser...@un...> - 2017-03-08 10:41:01
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Hi Jose, Pablo, Thanks a lot for suggestions. I didn't know that .pos files are in Tmp folder when Xmipp viewer is active. That's all I need, actually. Best regards, Sergey 2017-03-07 18:34 GMT+01:00 Jose Miguel de la Rosa Trevin < del...@gm...>: > Hi Serguey, > > There is an easy trick to get the .pos files associated to a > SetOfCoordinates (underlying .sqlite files). When you visualize a > SetOfCoordinates with Xmipp viewer, the corresponding .pos files are > generated in the project Tmp folder. Look there and search for its object > id. > > Anyway would be a good idea to have a more explicit export tool. > > Hope that helps > Jose Miguel > > On Mar 7, 2017 6:12 PM, "Pablo Conesa" <su...@bc...> > wrote: > >> Hi Sergey, >> >> I can't see anyway you can get the. pos file. Unless you get into the >> details of the sql. >> >> I'll check with the team if there is a workaround/hack to this and get >> back to you. >> >> I'll also annotate this as something useful to implement. >> >> All the best, Pablo. >> Scipion team >> >> Activo Mar, 7 Marzo at 1:21 PM , Sergey Nazarov <ser...@un...> >> Escrito: >> Hi, >> I would like to ask if it is possible to save coordinate files in .pos or >> any other format after Scipion-extract coordinates? Now they saved only in >> .sql format, but I would like to save them as normal text files for further >> usage. >> >> Best, >> Sergey Nazarov >> Biozentrum >> >> 55 >> >> ------------------------------------------------------------ >> ------------------ >> Announcing the Oxford Dictionaries API! The API offers world-renowned >> dictionary content that is easy and intuitive to access. Sign up for an >> account today to start using our lexical data to power your apps and >> projects. Get started today and enter our developer competition. >> http://sdm.link/oxford >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> |
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From: Juha H. <ju...@st...> - 2017-03-07 18:34:30
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Hello Developers, I currently pick filaments with helical symmetry using helixboxer of EMAN2 and save BOX files. Currently I process everything in Relion 2.0 using, but would be nice to do everything from Scipion. Once Relion 2.0 becomes available I guess we are one step closer. But I have a couple of questions what your plans are: - will Scipion support helical processing through Relion? - can filament coordinates be exported from BOX files? - could e2helixboxer GUI be supported? in addition to e2boxer? - will the in-plane angle retained from the filament end-points? Best wishes, Juha |
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From: Pablo C. <pc...@cn...> - 2017-03-07 17:52:52
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Many thanks Jose Miguel. On 07/03/17 18:34, Jose Miguel de la Rosa Trevin wrote: > Hi Serguey, > > There is an easy trick to get the .pos files associated to a > SetOfCoordinates (underlying .sqlite files). When you visualize a > SetOfCoordinates with Xmipp viewer, the corresponding .pos files are > generated in the project Tmp folder. Look there and search for its > object id. > > Anyway would be a good idea to have a more explicit export tool. > > Hope that helps > Jose Miguel > > On Mar 7, 2017 6:12 PM, "Pablo Conesa" <su...@bc... > <mailto:su...@bc...>> wrote: > > Hi Sergey, > > I can't see anyway you can get the. pos file. Unless you get into > the details of the sql. > > I'll check with the team if there is a workaround/hack to this and > get back to you. > > I'll also annotate this as something useful to implement. > > All the best, Pablo. > Scipion team > > Activo Mar, 7 Marzo at 1:21 PM , Sergey Nazarov > <ser...@un... <mailto:ser...@un...>> > Escrito: > Hi, > I would like to ask if it is possible to save coordinate files > in .pos or any other format after Scipion-extract coordinates? > Now they saved only in .sql format, but I would like to save > them as normal text files for further usage. > > Best, > Sergey Nazarov > Biozentrum > > 55 > > ------------------------------------------------------------------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up > for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > 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> > > > > ------------------------------------------------------------------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Jose M. de la R. T. <del...@gm...> - 2017-03-07 17:39:01
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Hi Dennis, I would suggest you to check the imported coordinates (Analyze results button) and ensure that coordinates match with expected particles. You can re-run the import protocol with X or Y flip until you get the expected results. Best regards, Jose Miguel On Mar 7, 2017 6:33 PM, "Dennis Thomas" <dt...@pr...> wrote: > > Using xmipp extract particles to extract particles from MRC aligned > frames, the coordinates are imported EMAN *.box files do I have to invert Y > or X or both. It doesn't seem to extract real particles. > > Thanks, > > Dennis > > > -- > Dr. Dennis Thomas > Cryo-EM Facility Manager > Center for Integrative Proteomics Research > Rutgers University > Phone: 848-445-5302 > > > ------------------------------------------------------------ > ------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Jose M. de la R. T. <del...@gm...> - 2017-03-07 17:34:11
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Hi Serguey, There is an easy trick to get the .pos files associated to a SetOfCoordinates (underlying .sqlite files). When you visualize a SetOfCoordinates with Xmipp viewer, the corresponding .pos files are generated in the project Tmp folder. Look there and search for its object id. Anyway would be a good idea to have a more explicit export tool. Hope that helps Jose Miguel On Mar 7, 2017 6:12 PM, "Pablo Conesa" <su...@bc...> wrote: > Hi Sergey, > > I can't see anyway you can get the. pos file. Unless you get into the > details of the sql. > > I'll check with the team if there is a workaround/hack to this and get > back to you. > > I'll also annotate this as something useful to implement. > > All the best, Pablo. > Scipion team > > Activo Mar, 7 Marzo at 1:21 PM , Sergey Nazarov <ser...@un...> > Escrito: > Hi, > I would like to ask if it is possible to save coordinate files in .pos or > any other format after Scipion-extract coordinates? Now they saved only in > .sql format, but I would like to save them as normal text files for further > usage. > > Best, > Sergey Nazarov > Biozentrum > > 55 > > ------------------------------------------------------------ > ------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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