scipion-users — Mailing list for Scipion users

Re: [scipion-users] Comparison of cryo-em maps

[Erney R. A. <era...@cn...>]

Hi Dmitry,

Right now we are working on something that can work. Exactly what  
would you like to compare?

Erney



Quoting Dmitry Semchonok <Sem...@gm...>:

> Dear colleagues,
>
> I have similar cryo-em maps that have also some differences.
> I want to compare them
>
> Is there a tool in SCIPION that can compare the cryo-em maps?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[scipion-users] Comparison of cryo-em maps

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

Dear colleagues,

I have similar cryo-em maps that have also some differences.
I want to compare them

Is there a tool in SCIPION that can compare the cryo-em maps?

Thank you!

Sincerely,
Dmitry

Re: [scipion-users] Coordinates extraction from relion to Scipion

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

Hi Dmitry,

You can import particles in scipion and then extract coordinates there. You
might be able to import coordinates into scipion directly from the
particles file but it will ignore any shifts.


Grigory.

On Fri, Feb 21, 2020, 10:51 Dmitry A. Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> I run the 3D refinement  with relion 3.0.8 and I want to extract the
> particle coordinates of
> this run to go on in SCIPION.
>
>
> How can I do that?
>
> Or is there some more straight forward way?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Coordinates extraction from relion to Scipion

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

Dear colleagues,

I run the 3D refinement  with relion 3.0.8 and I want to extract the 
particle coordinates of
this run to go on in SCIPION.


How can I do that?

Or is there some more straight forward way?

Thank you!

Sincerely,
Dmitry

Re: [scipion-users] xmipp3 - helical symmetry never finished

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

Dear Dmitry,

the only reason I can think of is that the search step (angle and Z) is 
very small, so that the program is exploring many different 
combinations. Can that be? If not, you may share with us the volume so 
that we can investigate ourselves what is happening.

Kind regards, Carlos Oscar

El 13/02/2020 a las 14:04, Dmitry Semchonok escribió:
> Dear colleagues,
>
> I have the issue running xmipp3 - helical symmetry protocol.
>
> The protocol starts but never ends no matter what parameters for the 
> threads/mpI I use.
>
> Does anyone knows about what is the problem?
>
> Thank  you!
>
> Sincerely,
> Dmitry
>
> /
> /
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Map is not visible in COOT

[Marta M. <mm...@cn...>]

Hi Dmitry,
Yes, you have to install CCP4 in addition to the plugin.
Cheers,
MARTA
Dmitry Semchonok <Sem...@gm...> escribió:

> Dear Marta,
>
> Thank you for your answer.
>
> The issue is that the post processed map is not visible by external COOT.
> So the map you can open without errors but you see nothing – we  
> tried to center it and to magnify/demagnify – nothing.
>
> The only hint that you get is the very wide map histogram in COOT  
> comparable to the other maps (as in my previous email).
>
>
>
>
> I would like to open it inside SCIPION. But currently, I got an  
> error message when I want to do the ccp4 - coot refinement that the  
> ccp4 is not installed (although I did it via SCIPION plugins):  
> Binary file does not exits. Please install CCP4 software suit.
>
> Do you know if I need to install CCP4 separately? Out of SCIPION?
>
> Thank you
>
> Sincerely,
> Dmitry
>
>> On 12. Feb 2020, at 19:48, Marta Martinez <mm...@cn...> wrote:
>>
>> Hi Dmitry,
>> I suppose that you are performing a modeling work inside Scipion.  
>> The reality is that we have never started the modeling process  
>> without importing the map (we haven't modified the output of the  
>> rest of the protocols to use directly the map generated yet). Even  
>> if you have generated the map in Scipion, import it to stablish the  
>> appropriate format and the origin of coordinates in the map header  
>> (you can choose in the protocol import volumes the origin, maybe  
>> yoy want to maintain the already existing origin or maybe you would  
>> like to have another one; by default we place maps centered at the  
>> origin of coordinates and you can check it in Chimera by pressing  
>> Analyze Results). If the map is properly located you have to be  
>> sure that the atomic model fits in the map to open Coot in Scipion  
>> and load map and model. By default Coot (in Scipion) requires a  
>> model to be launched, because we use Coot to visualize atomic  
>> structures or to perform the refinement of structures according to  
>> the map.
>>
>> Try to import the map and tell me if you still have problems to  
>> open the map in Coot. Is the name of the map in
>> the tap "Display Manager" in Coot?, Can you read the name of the  
>> map but you don't see anything? Does the model fit in the map?
>> I hope this help, otherwise clarify a little bit what you're doing,  
>> and if you're in or outside Scipion.
>>
>> Cheers,
>> MARTA
>>
>>
>> Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>>  
>> escribió:
>>
>>> Dear colleagues,
>>>
>>> I have cryo-em map obtained with relion in SCIPION.
>>>
>>> But when we want to open it in with COOT the map is not visible.  
>>> (Chimera can read it)
>>>
>>> Could you please give me any suggestions?
>>>
>>> Please see the image in the attachment the histogram differences —  
>>> on the left is readable file (made with relion itself) and from  
>>> the right is unreadable one (made by relion in SCIPION).
>>>
>>>
>>> Thank you
>>>
>>> Sincerely,
>>> Dmitry
>>
>>
>> --
>> Marta Martinez Gonzalez
>>
>> Biocomputing Unit (Lab B13)
>> National Center for Biotechnology-CSIC
>> Darwin, 3. Campus de la Universidad Autonoma de Madrid
>> 28049 Madrid. Spain
>> Tel:+34 915854510 Fax:+34 913720112
>> E-mail: mm...@cn... <mailto:mm...@cn...>
>>
>>
>>
>> _______________________________________________
>> 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>


-- 
Marta Martinez Gonzalez

Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mm...@cn...

Re: [scipion-users] Model building part of SCIPION

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

HI Dmitry, Scipion cannot install CCP4 software, you have to instal it 
yourself (you might already have it) and tell scipion where is it



  * *Binary files*

CCP4 binaries will/NOT/be installed automatically with the plugin. The 
independent installation of CCP4 software suite by the user is required 
before running the programs. Default installation path assumed 
is//usr/local/ccp4-7.0/; this path or any other of your preference has 
to be set in/CCP4_HOME/in/scipion.conf/. We recommend to install CCP4 
version 7.0.056 or higher.


Extracted from here: https://github.com/scipion-em/scipion-em-ccp4

On 13/2/20 11:12, Dmitry Semchonok wrote:
>
> Dear Marta,
>
> Apart from the fact that COOT doesn’t see the em-map it seems to be 
> some issue in with my installation of ccp4 & phenix via the SCIPION 
> plugin.
>
> When I use the plugin ccp4 in SCIPION I got an error
>
> 00001: DEPRECATION: Python 2.7 reached the end of its life on January 
> 1st, 2020. Please upgrade your Python as Python 2.7 is no longer 
> maintained. A future version of pip will drop support for Python 2.7. 
> More details about Python 2 support in pip, can be found at 
> https://pip.pypa.io/en/latest/development/release-process/#python-2-support
>
> 00002: DEPRECATION: Python 2.7 reached the end of its life on January 
> 1st, 2020. Please upgrade your Python as Python 2.7 is no longer 
> maintained. A future version of pip will drop support for Python 2.7. 
> More details about Python 2 support in pip, can be found at 
> https://pip.pypa.io/en/latest/development/release-process/#python-2-support
>
> 00003:   WARNING: You are using pip version 20.0.1; however, version 
> 20.0.2 is available.
>
> 00004:   You should consider upgrading via the 
> '/usr/local/scipion/v2.0.0/software/bin/python -m pip install 
> --upgrade pip' command.
>
> Sincerely,
>
> Dmitry
>
> By the way when we tried to use phenix externally – the protocol 
> finished without problems. So COOT has some issues with our map.
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] xmipp3 - helical symmetry never finished

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

Dear colleagues,

I have the issue running xmipp3 - helical symmetry protocol.

The protocol starts but never ends no matter what parameters for the threads/mpI I use.

Does anyone knows about what is the problem?

Thank  you!

Sincerely,
Dmitry

[scipion-users] Model building part of SCIPION

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

Dear Marta,

 

Apart from the fact that COOT doesn’t see the em-map it seems to be some issue in with my installation of ccp4 & phenix via the SCIPION plugin.

 

When I use the plugin ccp4 in SCIPION I got an error

 

00001:   DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support

00002:   DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support

00003:   WARNING: You are using pip version 20.0.1; however, version 20.0.2 is available.

00004:   You should consider upgrading via the '/usr/local/scipion/v2.0.0/software/bin/python -m pip install --upgrade pip' command.

 

 

Sincerely,

Dmitry

 

 By the way when we tried to use phenix externally – the protocol finished without problems. So COOT has some issues with our map.

Re: [scipion-users] Map is not visible in COOT

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

Dear Marta,

Thank you for your answer.

The issue is that the post processed map is not visible by external COOT.
So the map you can open without errors but you see nothing – we tried to center it and to magnify/demagnify – nothing.

The only hint that you get is the very wide map histogram in COOT comparable to the other maps (as in my previous email).


 

I would like to open it inside SCIPION. But currently, I got an error message when I want to do the ccp4 - coot refinement that the ccp4 is not installed (although I did it via SCIPION plugins): Binary file does not exits. Please install CCP4 software suit.

Do you know if I need to install CCP4 separately? Out of SCIPION?

Thank you

Sincerely,
Dmitry

> On 12. Feb 2020, at 19:48, Marta Martinez <mm...@cn...> wrote:
> 
> Hi Dmitry,
> I suppose that you are performing a modeling work inside Scipion. The reality is that we have never started the modeling process without importing the map (we haven't modified the output of the rest of the protocols to use directly the map generated yet). Even if you have generated the map in Scipion, import it to stablish the appropriate format and the origin of coordinates in the map header (you can choose in the protocol import volumes the origin, maybe yoy want to maintain the already existing origin or maybe you would like to have another one; by default we place maps centered at the origin of coordinates and you can check it in Chimera by pressing Analyze Results). If the map is properly located you have to be sure that the atomic model fits in the map to open Coot in Scipion and load map and model. By default Coot (in Scipion) requires a model to be launched, because we use Coot to visualize atomic structures or to perform the refinement of structures according to the map.
> 
> Try to import the map and tell me if you still have problems to open the map in Coot. Is the name of the map in
> the tap "Display Manager" in Coot?, Can you read the name of the map but you don't see anything? Does the model fit in the map?
> I hope this help, otherwise clarify a little bit what you're doing, and if you're in or outside Scipion.
> 
> Cheers,
> MARTA
> 
> 
> Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> escribió:
> 
>> Dear colleagues,
>> 
>> I have cryo-em map obtained with relion in SCIPION.
>> 
>> But when we want to open it in with COOT the map is not visible. (Chimera can read it)
>> 
>> Could you please give me any suggestions?
>> 
>> Please see the image in the attachment the histogram differences — on the left is readable file (made with relion itself) and from the right is unreadable one (made by relion in SCIPION).
>> 
>> 
>> Thank you
>> 
>> Sincerely,
>> Dmitry
> 
> 
> -- 
> Marta Martinez Gonzalez
> 
> Biocomputing Unit (Lab B13)
> National Center for Biotechnology-CSIC
> Darwin, 3. Campus de la Universidad Autonoma de Madrid
> 28049 Madrid. Spain
> Tel:+34 915854510 Fax:+34 913720112
> E-mail: mm...@cn... <mailto:mm...@cn...>
> 
> 
> 
> _______________________________________________
> 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>

Re: [scipion-users] Map is not visible in COOT

[Marta M. <mm...@cn...>]

Hi Dmitry,
I suppose that you are performing a modeling work inside Scipion. The  
reality is that we have never started the modeling process without  
importing the map (we haven't modified the output of the rest of the  
protocols to use directly the map generated yet). Even if you have  
generated the map in Scipion, import it to stablish the appropriate  
format and the origin of coordinates in the map header (you can choose  
in the protocol import volumes the origin, maybe yoy want to maintain  
the already existing origin or maybe you would like to have another  
one; by default we place maps centered at the origin of coordinates  
and you can check it in Chimera by pressing Analyze Results). If the  
map is properly located you have to be sure that the atomic model fits  
in the map to open Coot in Scipion and load map and model. By default  
Coot (in Scipion) requires a model to be launched, because we use Coot  
to visualize atomic structures or to perform the refinement of  
structures according to the map.

Try to import the map and tell me if you still have problems to open  
the map in Coot. Is the name of the map in
the tap "Display Manager" in Coot?, Can you read the name of the map  
but you don't see anything? Does the model fit in the map?
I hope this help, otherwise clarify a little bit what you're doing,  
and if you're in or outside Scipion.

Cheers,
MARTA


Dmitry Semchonok <Sem...@gm...> escribió:

> Dear colleagues,
>
> I have cryo-em map obtained with relion in SCIPION.
>
> But when we want to open it in with COOT the map is not visible.  
> (Chimera can read it)
>
> Could you please give me any suggestions?
>
> Please see the image in the attachment the histogram differences —  
> on the left is readable file (made with relion itself) and from the  
> right is unreadable one (made by relion in SCIPION).
>
>
> Thank you
>
> Sincerely,
> Dmitry


-- 
Marta Martinez Gonzalez

Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mm...@cn...

[scipion-users] Map is not visible in COOT

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

Dear colleagues,

I have cryo-em map obtained with relion in SCIPION.

But when we want to open it in with COOT the map is not visible. (Chimera can read it)

Could you please give me any suggestions?

Please see the image in the attachment the histogram differences — on the left is readable file (made with relion itself) and from the right is unreadable one (made by relion in SCIPION).


Thank you 

Sincerely,
Dmitry

Re: [scipion-users] Simmetry definition

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

Dear Dmitry,

it is true that in Scipion there is no true helical plugin. In Xmipp we 
have done some explorations (look for "Helical" with CTRL-F and Helical 
parameters should appear). That is a protocol to find and apply the 
helical parameters to a c1 volume. The exploration we did was 
alternating c1 one iteration of reconstructions with Xmipp highres, and 
a search/symmetrization. According to our single user of this protocol 
:-), the symmetrization of Xmipp was better than anything else he could 
compare. We did not pursue too much this line, so that we don't know if 
the overall result is better than other more specific packages (probably 
not, for instance we do not keep track of pieces coming from the same 
helix, which would reduce the uncertainty about alignment), and 
certainly it is inconvenient because of the need to alternate protocols. 
We found it very useful in order to escape from incorrect structures in 
which other packages were getting trapped.

Kind regards, Carlos Oscar

On 21/1/2020 18:20, Dmitry Semchonok wrote:
> Dear colleagues,
>
> Does any one work with the helices using SCIPION?
> If yes then is there a walkthrough/manual?
> As far as I remember the helix structure analysis currently is not implemented into the workflow.
>
> How to define the symmetry of the helix/particle? is there any tool for that?
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] slow GUI

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

Dear Dario,

thank you for sharing your solution. I also use Ubuntu 18, regularly and 
I don't have that problem. It might be, as you say, some particular 
interaction between the particular installation and the machine.

Kind regards, Carlos Oscar

On 23/1/2020 14:36, Dario Saczko-Brack via scipion-users wrote:
>
> I have found a rather strange solution:
>
> The GUI works now as fast as I would wish, however, only when I press 
> the "Alt" button on my keyboard... The GUI window opens and stays 
> grey, until I hit "Alt". Or a window doesnt even open, but as soon as 
> I hit "Alt", it opens...
>
> I have no idea what is the underlying issue here, maybe, just maybe, 
> anyone has encountered this as well. It is definitely something with 
> Ubuntu 18 on my machine, as there is another problem (when I start my 
> pc, after approx 10-60 min, it gets stuck and reboots, after that its 
> fine...). I will give it a try in Ubuntu-forums :)
>
> Best
>
> Dario
>
>
>
> On 21.01.20 18:10, Jose Maria Carazo wrote:
>> Dear Dario
>>
>> I am sure that the more technical people in the list will help you. I 
>> have Scipion installed in my Dell 5530 and I have no problems with 
>> the GUI
>>
>> Wbw..JM
>>
>> On Tue, Jan 21, 2020 at 1:15 PM Jose Miguel de la Rosa Trevin 
>> <del...@gm... <mailto:del...@gm...>> wrote:
>>
>>     Hi Dario,
>>
>>     How is the hard drive that you are using? Local or mounted
>>     through the network.
>>     Anyway, I haven't seen so slow the GUI as you mention. In our
>>     case, we have the
>>     installation of the software in a network filesystem and it
>>     usually take quite a bit of time
>>     loading python libraries, but only the first time you open a window.
>>
>>     Best,
>>     Jose Miguel
>>
>>
>>
>>     On Tue, Jan 21, 2020 at 12:52 PM Dario Saczko-Brack via
>>     scipion-users <sci...@li...
>>     <mailto:sci...@li...>> wrote:
>>
>>         Hi all,
>>
>>         I have a question regarding the speed of the GUI. Almost each
>>         window
>>         takes quite a long time to open (from some seconds up to several
>>         minutes). Sometimes it helps to kill scipion and reopen it,
>>         but this is
>>         not the most convenient workaround.
>>
>>         Are there any settings that can be made so it runs smoother
>>         on our
>>         workstation:
>>
>>         Intel® Xeon(R) CPU E5-2698 v3 @ 2.30GHz × 32
>>
>>         2x RAM DDR4 REG 32GB
>>
>>         2x GeForce GTX 1070
>>
>>
>>         Thanks in advance
>>
>>         Best
>>
>>         Dario
>>
>>
>>
>>
>>         _______________________________________________
>>         scipion-users mailing list
>>         sci...@li...
>>         <mailto:sci...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...
>>     <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>>
>>
>> -- 
>> Prof. Jose-Maria Carazo
>> Biocomputing Unit, Head, CNB-CSIC
>> Spanish National Center for Biotechnology
>> Darwin 3, Universidad Autonoma de Madrid
>> 28049 Madrid, Spain
>>
>>
>> Cell: +34639197980
>>
>>
>> _______________________________________________
>> 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] HELICAL RECONSTRUCTION software// symmetry

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

Great news Jose Miguel!

Meanwhile, does anyone know where to find the clear manual for the relion helical reconstruction as for SCIPION one?

Sincerely,
Dmitry


> On 23. Jan 2020, at 15:43, Dario Saczko-Brack via scipion-users <sci...@li...> wrote:
> 
> 
>> We are planning to go back to this and implement now as a proper helical plugin. 
> That is great, I am looking forward to that :)
> 
> On 23.01.20 15:41, Jose Miguel de la Rosa Trevin wrote:
>> Hi Dmitry, 
>> 
>> Dario already suggested some of the packages that have helical tools.
>> It is also correct that there are not any of these implemented in Scipion right now.
>> Together with Juha Huiskone we started to implement the data model for helical processing some time ago.
>> We are planning to go back to this and implement now as a proper helical plugin. 
>> 
>> Best regards,
>> Jose Miguel
>> 
>> 
>> On Thu, Jan 23, 2020 at 3:36 PM Dario Saczko-Brack via scipion-users <sci...@li... <mailto:sci...@li...>> wrote:
>> Hi Dmitry, 
>> 
>> there are some softwares that fokus on helical reconstruction: Spring <http://www.sachse.embl.de/emspring/>, IHRSR <https://bakerlab.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf>, Relion has also helical processing <https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Helical_processing#Particle_extraction> implemented. I am not sure, but so far scipion doesnt have procedures for helical processing included (correct me if I am wrong).
>> 
>> Best
>> 
>> Dario
>> 
>> 
>> 
>> 
>> 
>> On 23.01.20 15:26, Dmitry Semchonok wrote:
>>>  <> <> <>Dear colleagues,
>>> 
>>>  
>>> Does anyone have recommendations for HELICAL RECONSTRUCTION image processing software?
>>> 
>>>  Can SCIPION process it in some way?
>>> 
>>>  
>>>  
>>> Another question about the symmetry – how to find the symmetry of your particle?
>>> 
>>> Is there a program where you can put your 2D classes and get come guess for the symmetry?
>>> 
>>>  
>>> Sincerely,
>>> 
>>> Dmitry 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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>
>> _______________________________________________
>> 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>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] HELICAL RECONSTRUCTION software// symmetry

[Dario Saczko-B. <dar...@go...>]

> We are planning to go back to this and implement now as a proper 
> helical plugin. 
That is great, I am looking forward to that :)

On 23.01.20 15:41, Jose Miguel de la Rosa Trevin wrote:
> Hi Dmitry,
>
> Dario already suggested some of the packages that have helical tools.
> It is also correct that there are not any of these implemented in 
> Scipion right now.
> Together with Juha Huiskone we started to implement the data model for 
> helical processing some time ago.
> We are planning to go back to this and implement now as a proper 
> helical plugin.
>
> Best regards,
> Jose Miguel
>
>
> On Thu, Jan 23, 2020 at 3:36 PM Dario Saczko-Brack via scipion-users 
> <sci...@li... 
> <mailto:sci...@li...>> wrote:
>
>     Hi Dmitry,
>
>     there are some softwares that fokus on helical reconstruction:
>     Spring <http://www.sachse.embl.de/emspring/>, IHRSR
>     <https://bakerlab.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf>,
>     Relion has also helical processing
>     <https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Helical_processing#Particle_extraction>
>     implemented. I am not sure, but so far scipion doesnt have
>     procedures for helical processing included (correct me if I am wrong).
>
>     Best
>
>     Dario
>
>
>
>     On 23.01.20 15:26, Dmitry Semchonok wrote:
>>
>>     Dear colleagues,
>>
>>     Does anyone have recommendations for HELICAL RECONSTRUCTION image
>>     processing software?
>>
>>     Can SCIPION process it in some way?
>>
>>     Another question about the symmetry – how to find the symmetry of
>>     your particle?
>>
>>     Is there a program where you can put your 2D classes and get come
>>     guess for the symmetry?
>>
>>     Sincerely,
>>
>>     Dmitry
>>
>>
>>
>>     _______________________________________________
>>     scipion-users mailing list
>>     sci...@li...  <mailto:sci...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] HELICAL RECONSTRUCTION software// symmetry

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

Hi Dmitry,

Dario already suggested some of the packages that have helical tools.
It is also correct that there are not any of these implemented in Scipion
right now.
Together with Juha Huiskone we started to implement the data model for
helical processing some time ago.
We are planning to go back to this and implement now as a proper helical
plugin.

Best regards,
Jose Miguel


On Thu, Jan 23, 2020 at 3:36 PM Dario Saczko-Brack via scipion-users <
sci...@li...> wrote:

> Hi Dmitry,
>
> there are some softwares that fokus on helical reconstruction: Spring
> <http://www.sachse.embl.de/emspring/>, IHRSR
> <https://bakerlab.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf>, Relion has
> also helical processing
> <https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Helical_processing#Particle_extraction>
> implemented. I am not sure, but so far scipion doesnt have procedures for
> helical processing included (correct me if I am wrong).
>
> Best
>
> Dario
>
>
>
> On 23.01.20 15:26, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
>
>
> Does anyone have recommendations for HELICAL RECONSTRUCTION image
> processing software?
>
>  Can SCIPION process it in some way?
>
>
>
>
>
> Another question about the symmetry – how to find the symmetry of your
> particle?
>
> Is there a program where you can put your 2D classes and get come guess
> for the symmetry?
>
>
>
> Sincerely,
>
> Dmitry
>
>
> _______________________________________________
> scipion-users mailing lis...@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] HELICAL RECONSTRUCTION software// symmetry

[Dario Saczko-B. <dar...@go...>]

Hi Dmitry,

there are some softwares that fokus on helical reconstruction: Spring 
<http://www.sachse.embl.de/emspring/>, IHRSR 
<https://bakerlab.ucsd.edu/programs/IHRSR++tutorial_v1.5.pdf>, Relion 
has also helical processing 
<https://www3.mrc-lmb.cam.ac.uk/relion//index.php?title=Helical_processing#Particle_extraction> 
implemented. I am not sure, but so far scipion doesnt have procedures 
for helical processing included (correct me if I am wrong).

Best

Dario



On 23.01.20 15:26, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> Does anyone have recommendations for HELICAL RECONSTRUCTION image 
> processing software?
>
> Can SCIPION process it in some way?
>
> Another question about the symmetry – how to find the symmetry of your 
> particle?
>
> Is there a program where you can put your 2D classes and get come 
> guess for the symmetry?
>
> Sincerely,
>
> Dmitry
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

[scipion-users] HELICAL RECONSTRUCTION software// symmetry

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

 <> <> <>Dear colleagues,

 

Does anyone have recommendations for HELICAL RECONSTRUCTION image processing software?

 Can SCIPION process it in some way?

 

 

Another question about the symmetry – how to find the symmetry of your particle?

Is there a program where you can put your 2D classes and get come guess for the symmetry?

 

Sincerely,

Dmitry 

Re: [scipion-users] slow GUI

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

Thanks for the update Dario!

I haven't experienced that myself. I'm sorry not to be of much help here.


On Thu, Jan 23, 2020 at 11:38 AM Dario Saczko-Brack via scipion-users <
sci...@li...> wrote:

> I have found a rather strange solution:
>
> The GUI works now as fast as I would wish, however, only when I press the
> "Alt" button on my keyboard... The GUI window opens and stays grey, until I
> hit "Alt". Or a window doesnt even open, but as soon as I hit "Alt", it
> opens...
>
> I have no idea what is the underlying issue here, maybe, just maybe,
> anyone has encountered this as well. It is definitely something with Ubuntu
> 18 on my machine, as there is another problem (when I start my pc, after
> approx 10-60 min, it gets stuck and reboots, after that its fine...). I
> will give it a try in Ubuntu-forums :)
>
> Best
>
> Dario
>
>
>
> On 21.01.20 18:10, Jose Maria Carazo wrote:
>
> Dear Dario
>
> I am sure that the more technical people in the list will help you. I have
> Scipion installed in my Dell 5530 and I have no problems with the GUI
>
> Wbw..JM
>
> On Tue, Jan 21, 2020 at 1:15 PM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Hi Dario,
>>
>> How is the hard drive that you are using? Local or mounted through the
>> network.
>> Anyway, I haven't seen so slow the GUI as you mention. In our case, we
>> have the
>> installation of the software in a network filesystem and it usually take
>> quite a bit of time
>> loading python libraries, but only the first time you open a window.
>>
>> Best,
>> Jose Miguel
>>
>>
>>
>> On Tue, Jan 21, 2020 at 12:52 PM Dario Saczko-Brack via scipion-users <
>> sci...@li...> wrote:
>>
>>> Hi all,
>>>
>>> I have a question regarding the speed of the GUI. Almost each window
>>> takes quite a long time to open (from some seconds up to several
>>> minutes). Sometimes it helps to kill scipion and reopen it, but this is
>>> not the most convenient workaround.
>>>
>>> Are there any settings that can be made so it runs smoother on our
>>> workstation:
>>>
>>> Intel® Xeon(R) CPU E5-2698 v3 @ 2.30GHz × 32
>>>
>>> 2x RAM DDR4 REG 32GB
>>>
>>> 2x GeForce GTX 1070
>>>
>>>
>>> Thanks in advance
>>>
>>> Best
>>>
>>> Dario
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
>
> --
> Prof. Jose-Maria Carazo
> Biocomputing Unit, Head, CNB-CSIC
> Spanish National Center for Biotechnology
> Darwin 3, Universidad Autonoma de Madrid
> 28049 Madrid, Spain
>
>
> Cell: +34639197980
>
>
> _______________________________________________
> scipion-users mailing lis...@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] slow GUI

[Dario Saczko-B. <dar...@go...>]

I have found a rather strange solution:

The GUI works now as fast as I would wish, however, only when I press 
the "Alt" button on my keyboard... The GUI window opens and stays grey, 
until I hit "Alt". Or a window doesnt even open, but as soon as I hit 
"Alt", it opens...

I have no idea what is the underlying issue here, maybe, just maybe, 
anyone has encountered this as well. It is definitely something with 
Ubuntu 18 on my machine, as there is another problem (when I start my 
pc, after approx 10-60 min, it gets stuck and reboots, after that its 
fine...). I will give it a try in Ubuntu-forums :)

Best

Dario



On 21.01.20 18:10, Jose Maria Carazo wrote:
> Dear Dario
>
> I am sure that the more technical people in the list will help you. I 
> have Scipion installed in my Dell 5530 and I have no problems with the GUI
>
> Wbw..JM
>
> On Tue, Jan 21, 2020 at 1:15 PM Jose Miguel de la Rosa Trevin 
> <del...@gm... <mailto:del...@gm...>> wrote:
>
>     Hi Dario,
>
>     How is the hard drive that you are using? Local or mounted through
>     the network.
>     Anyway, I haven't seen so slow the GUI as you mention. In our
>     case, we have the
>     installation of the software in a network filesystem and it
>     usually take quite a bit of time
>     loading python libraries, but only the first time you open a window.
>
>     Best,
>     Jose Miguel
>
>
>
>     On Tue, Jan 21, 2020 at 12:52 PM Dario Saczko-Brack via
>     scipion-users <sci...@li...
>     <mailto:sci...@li...>> wrote:
>
>         Hi all,
>
>         I have a question regarding the speed of the GUI. Almost each
>         window
>         takes quite a long time to open (from some seconds up to several
>         minutes). Sometimes it helps to kill scipion and reopen it,
>         but this is
>         not the most convenient workaround.
>
>         Are there any settings that can be made so it runs smoother on
>         our
>         workstation:
>
>         Intel® Xeon(R) CPU E5-2698 v3 @ 2.30GHz × 32
>
>         2x RAM DDR4 REG 32GB
>
>         2x GeForce GTX 1070
>
>
>         Thanks in advance
>
>         Best
>
>         Dario
>
>
>
>
>         _______________________________________________
>         scipion-users mailing list
>         sci...@li...
>         <mailto:sci...@li...>
>         https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> -- 
> Prof. Jose-Maria Carazo
> Biocomputing Unit, Head, CNB-CSIC
> Spanish National Center for Biotechnology
> Darwin 3, Universidad Autonoma de Madrid
> 28049 Madrid, Spain
>
>
> Cell: +34639197980
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Problem with Scipion and Xmipp

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

Great to hear it's fixed now!

We are working to make this more intuitive in the next version.

Thanks to you for reporting.


Cheers!

<http://ucm.es/>

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

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



On Tue, Jan 21, 2020 at 9:56 AM Dario Saczko-Brack <
dar...@go...> wrote:

> Hi David,
>
> that was the "trick". I have installed the plugin, without going back to
> the plugin manager, expanding scipion-em-xmipp and install one of the
> binary. Now it seems to work, at least there is no error message upon
> startup. The tests including xmipp-procedures also pass without error.
> Thanks again.
>
> Also thank You Wolfgang and Grigory forthe support.
>
> Best
>
> Dario
>
>
> On 20.01.20 21:36, David Maluenda wrote:
>
> Hi Dario and Scipion-Users,
>
> It seems that Xmipp plugin is installed but not the software below. Once
> the Xmipp plugin is installed, the Xmipp software appears below the Xmipp
> plugin in the plugin manager. You should choose a binary (for Centos or For
> Debian distros) o the sources to complie (other distros). More informarion
> can be found in the link that Gregory placed.
>
>
> Thanks!
>
> _____
> Dr. David Maluenda Niubó
> 619.029.310 - dma...@cn...
> Centro Nacional de Biotecnología - CSIC
> BioComputing Unit
>
> El lun., 20 ene. 2020 17:45, Grigory Sharov <sha...@gm...>
> escribió:
>
>> Hi Dario,
>>
>> It may as well be that xmipp installation through Plugin manager has
>> failed, you should check the Plugin.err or log file for details. If that's
>> the case you might try to install xmipp
>> <https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins>
>> from command line.
>>
>> Best regards,
>> Grigory
>>
>>
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228 <+44%201223%20267228>
>> e-mail: gs...@mr...
>>
>>
>> On Mon, Jan 20, 2020 at 4:37 PM Lugmayr, Wolfgang <w.l...@uk...>
>> wrote:
>>
>>> hi,
>>>
>>> i extended the original scipion.conf with some site information and call
>>> it like:
>>> scipion --config scipion_cssb.conf
>>>
>>> the package section below for example is not in the original scipion.conf
>>>
>>> [PACKAGES]
>>> EM_ROOT = software/em
>>> MOTIONCOR2_BIN = MotionCor2_1.2.6-Cuda101
>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda-10.1/lib64
>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.2.6
>>> XMIPP_HOME = %(EM_ROOT)s/xmipp
>>>
>>> maybe this helps?
>>>
>>> cheers,
>>> wolfgang
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: "Mailing list for Scipion users" <
>>> sci...@li...>
>>> To: "Mailing list for Scipion users" <
>>> sci...@li...>
>>> Cc: "Dario Saczko-Brack" <dar...@go...>
>>> Sent: Monday, 20 January, 2020 16:57:23
>>> Subject: [scipion-users] Problem with Scipion and Xmipp
>>>
>>> Hi all,
>>>
>>> I have a question about the xmipp within scipion, as it seems not to
>>> work properly on my machine. I always get the error message upon the
>>> scipion start, although I have installed xmipp using the plugin manager
>>> (and already several times removed+installed again):
>>>
>>> >  >>> WARNING: Xmipp binaries not found. Ghost active.....BOOOOOO!
>>> >   > Please install Xmipp to get full functionality.
>>> > (Configuration->Plugins->scipion-em-xmipp in Scipion manager window)
>>>
>>>
>>> Does anyone had this problem too and knows how to deal with it? If there
>>> are any more information you need, let me know.
>>>
>>>
>>> Thanks in advance
>>>
>>> Dario
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>

Re: [scipion-users] slow GUI

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

Dear Dario

I am sure that the more technical people in the list will help you. I have
Scipion installed in my Dell 5530 and I have no problems with the GUI

Wbw..JM

On Tue, Jan 21, 2020 at 1:15 PM Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Hi Dario,
>
> How is the hard drive that you are using? Local or mounted through the
> network.
> Anyway, I haven't seen so slow the GUI as you mention. In our case, we
> have the
> installation of the software in a network filesystem and it usually take
> quite a bit of time
> loading python libraries, but only the first time you open a window.
>
> Best,
> Jose Miguel
>
>
>
> On Tue, Jan 21, 2020 at 12:52 PM Dario Saczko-Brack via scipion-users <
> sci...@li...> wrote:
>
>> Hi all,
>>
>> I have a question regarding the speed of the GUI. Almost each window
>> takes quite a long time to open (from some seconds up to several
>> minutes). Sometimes it helps to kill scipion and reopen it, but this is
>> not the most convenient workaround.
>>
>> Are there any settings that can be made so it runs smoother on our
>> workstation:
>>
>> Intel® Xeon(R) CPU E5-2698 v3 @ 2.30GHz × 32
>>
>> 2x RAM DDR4 REG 32GB
>>
>> 2x GeForce GTX 1070
>>
>>
>> Thanks in advance
>>
>> Best
>>
>> Dario
>>
>>
>>
>>
>> _______________________________________________
>> 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
>


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


Cell: +34639197980

[scipion-users] Simmetry definition

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

Dear colleagues,

Does any one work with the helices using SCIPION?
If yes then is there a walkthrough/manual? 
As far as I remember the helix structure analysis currently is not implemented into the workflow.

How to define the symmetry of the helix/particle? is there any tool for that?


Thank you

Sincerely,
Dmitry 

Re: [scipion-users] slow GUI

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

Hi Dario,

How is the hard drive that you are using? Local or mounted through the
network.
Anyway, I haven't seen so slow the GUI as you mention. In our case, we have
the
installation of the software in a network filesystem and it usually take
quite a bit of time
loading python libraries, but only the first time you open a window.

Best,
Jose Miguel



On Tue, Jan 21, 2020 at 12:52 PM Dario Saczko-Brack via scipion-users <
sci...@li...> wrote:

> Hi all,
>
> I have a question regarding the speed of the GUI. Almost each window
> takes quite a long time to open (from some seconds up to several
> minutes). Sometimes it helps to kill scipion and reopen it, but this is
> not the most convenient workaround.
>
> Are there any settings that can be made so it runs smoother on our
> workstation:
>
> Intel® Xeon(R) CPU E5-2698 v3 @ 2.30GHz × 32
>
> 2x RAM DDR4 REG 32GB
>
> 2x GeForce GTX 1070
>
>
> Thanks in advance
>
> Best
>
> Dario
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>