emspring

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Spring is a single-particle based helical reconstruction package and has been used to determine 3D structures of a variety of highly ordered and less ordered specimens from electron micrographs. Spring is currently developed in the Sachse lab at the Ernst-Ruska Centre of Forschungszentrum Jülich for the Unix operating systems of MacOSX and Linux.

When you post any issues of the software package:

1. Provide the following output to us:

% spring --version && springenv e2version.py

2. Provide a proper signature to your message indicating your institution and research group

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7/21/22

micexam stops after initialising

Emspring (0.87.1724) OS Name: Centos Linux 7.9 OS Type: 64-bit I am new to the EM field and I just

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micexam stops after initialising

Emspring (0.87.1724) OS Name: Centos Linux 7.9 OS Type: 64-bit I am new to the EM field and I just

7/21/22

Christer Edvardsson, Carsten Sachse2

4/4/22

micctfdetermine crash report

Dear Christer, Could you attach the report .log file of MICCTFDETERMINE? Are the executable of

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micctfdetermine crash report

Dear Christer, Could you attach the report .log file of MICCTFDETERMINE? Are the executable of

4/4/22

Christer Edvardsson, Carsten Sachse4

4/1/22

What version is recommended for installation on Ubuntu?

Dear Christer, Thanks for posting the message and following up on the issue. We will need to test the

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What version is recommended for installation on Ubuntu?

Dear Christer, Thanks for posting the message and following up on the issue. We will need to test the

4/1/22

1/12/21

Spring website moved to https://spring.fz-juelich.de/

Dear Spring users, My lab has moved some time ago to the Ernst-Ruska Centre at the Forschungszentrum

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Spring website moved to https://spring.fz-juelich.de/

Dear Spring users, My lab has moved some time ago to the Ernst-Ruska Centre at the Forschungszentrum

1/12/21

Isabelle Gordon, Carsten Sachse2

6/22/20

Using RELION coordinates in SPRING segment

Hi Isabelle, We found an older python conversion script. You can import the star coordinates by

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Using RELION coordinates in SPRING segment

Hi Isabelle, We found an older python conversion script. You can import the star coordinates by

6/22/20

Isabelle Gordon, Carsten Sachse2

3/12/20

Lustre-based storage and spring.db file

Hi Isabelle, You are the first person reporting such a compatibility issue with Lustre-based file

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Lustre-based storage and spring.db file

Hi Isabelle, You are the first person reporting such a compatibility issue with Lustre-based file

3/12/20

Martin, Carsten Sachse4

2/18/20

Spring installation on MacOS 10.14

Dear Martin, I am glad to hear the proposed fix worked! This is a relatively easy fix. Best wishes,

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Spring installation on MacOS 10.14

Dear Martin, I am glad to hear the proposed fix worked! This is a relatively easy fix. Best wishes,

2/18/20

Yangqi Gu, Carsten Sachse2

5/14/19

Install Spring with mpi on cluster

Dear Yangqi, In principle, the provided binary install will work on various cluster systems, ie.

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Install Spring with mpi on cluster

Dear Yangqi, In principle, the provided binary install will work on various cluster systems, ie.

5/14/19

Oda Toshiyuki, Carsten Sachse3

3/22/19

michelixtract problem

Dear Carsten, The error was about wrong value of Tile size power spectrum. ==== ValueError: Chosen

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michelixtract problem

Dear Carsten, The error was about wrong value of Tile size power spectrum. ==== ValueError: Chosen

3/22/19

Neville Bethel, Carsten Sachse2

9/26/18

michelixtrace reference cropped

Dear Neville, Your cross correlation map does not show a high correlation trace, which is why

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michelixtrace reference cropped

Dear Neville, Your cross correlation map does not show a high correlation trace, which is why

9/26/18

jrj...@gmail.com, Carsten Sachse2

8/17/18

segmentexam on extracted particles from RELION

Dear John, Unfortunately, there is currently no simple way to convert the particles.star into the

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segmentexam on extracted particles from RELION

Dear John, Unfortunately, there is currently no simple way to convert the particles.star into the

8/17/18

Hiroshi Imai, Carsten Sachse2

6/11/18

How to handle 2- or 3- start helix using the SPRING software?

Dear Hiroshi, On Thursday, 7 June 2018 13:06:10 UTC+2, Hiroshi Imai wrote: Dear Carsten The SPRING

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How to handle 2- or 3- start helix using the SPRING software?

Dear Hiroshi, On Thursday, 7 June 2018 13:06:10 UTC+2, Hiroshi Imai wrote: Dear Carsten The SPRING

6/11/18

Hiroshi Imai, Carsten Sachse3

5/15/18

How to determine pixel size? Why do you include nano gold particles in your specimen?

Dear Carsten Thank you very much for your clear reply. It is fantastic to receive the answers from

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How to determine pixel size? Why do you include nano gold particles in your specimen?

Dear Carsten Thank you very much for your clear reply. It is fantastic to receive the answers from

5/15/18

Hiroshi Imai, Carsten Sachse7

5/4/18

Installation trouble in mac os x 10.13.3

Dear Carsten It is good news. I have completed all the tutorial of the 3D TMV reconstruction as a

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Installation trouble in mac os x 10.13.3

Dear Carsten It is good news. I have completed all the tutorial of the 3D TMV reconstruction as a

5/4/18

Dawid Zyla, Carsten Sachse4

4/19/18

Spring python problem - installation issue

Dear all, David has confirmed that it works. Please, be aware I included the patched

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Spring python problem - installation issue

Dear all, David has confirmed that it works. Please, be aware I included the patched

4/19/18

Ambroise Desfosses, Carsten Sachse3

3/14/18

Input reference volume

Dear Carsten, yes it does answer the question, thanks. Ambroise Le mardi 13 mars 2018 14:37:29 UTC+1,

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Input reference volume

Dear Carsten, yes it does answer the question, thanks. Ambroise Le mardi 13 mars 2018 14:37:29 UTC+1,

3/14/18

Juha, Carsten Sachse2

3/13/18

Siggridexplore popup window does not open

Hi Juha, I assume this is an error in the composition of the grid.db Is it possible that your

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Siggridexplore popup window does not open

Hi Juha, I assume this is an error in the composition of the grid.db Is it possible that your

3/13/18

Colin Deniston, Carsten Sachse3

2/9/18

2D Class Average Particles

Thanks for the info! On Thursday, February 8, 2018 at 1:56:24 AM UTC-8, Carsten Sachse wrote: Dear

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2D Class Average Particles

Thanks for the info! On Thursday, February 8, 2018 at 1:56:24 AM UTC-8, Carsten Sachse wrote: Dear

2/9/18

Colin Deniston, Carsten Sachse7

1/25/18

SPRING Stalling Error on Segment and Michelixtrace Jobs

Dear Collin, We had another look at your parameter files and certified that they are running. It

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SPRING Stalling Error on Segment and Michelixtrace Jobs

Dear Collin, We had another look at your parameter files and certified that they are running. It

1/25/18

12/18/17

Spring 0.86.1661 release

Dear Spring users, It is a pleasure to announce a new release of the Spring software suite for single

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Spring 0.86.1661 release

Dear Spring users, It is a pleasure to announce a new release of the Spring software suite for single

12/18/17

Luca Jovine, Carsten Sachse11

10/16/17

Trying to install SPRING under Mac OS 10.12.6

Hi again, This indeed allowed the build to go further, but I also had to add: cd fetch; curl --remote

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Trying to install SPRING under Mac OS 10.12.6

Hi again, This indeed allowed the build to go further, but I also had to add: cd fetch; curl --remote

10/16/17

10/10/17

Spring update 0.85.1617

Dear Spring users, I would like to announce another update of Spring. Most important updates include:

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Spring update 0.85.1617

Dear Spring users, I would like to announce another update of Spring. Most important updates include:

10/10/17

Colin Deniston, Carsten Sachse2

9/19/17

McHelixTrace Questions

Dear Colin, Be sure to use the latest version of Spring, ie. version 0.85.1617 as of now. On Monday,

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McHelixTrace Questions

Dear Colin, Be sure to use the latest version of Spring, ie. version 0.85.1617 as of now. On Monday,

9/19/17

David Haselbach, Carsten Sachse2

8/7/17

no such file or directory error

Dear David, Thank you for posting the error message. Please refer to a previous post: https://groups.

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no such file or directory error

Dear David, Thank you for posting the error message. Please refer to a previous post: https://groups.

8/7/17

David Haselbach, Carsten Sachse2

8/7/17

Installation Problem

Dear David, I will post a Spring update to the installation problem very soon. For those who have

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Installation Problem

Dear David, I will post a Spring update to the installation problem very soon. For those who have

8/7/17

Andrew Kehr, Carsten Sachse2

6/7/17

SegGridExplore output

Dear Andrew, The peakedness of the cross correlation landscape depends completely on the features of

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SegGridExplore output

Dear Andrew, The peakedness of the cross correlation landscape depends completely on the features of

6/7/17

David Hoover, Carsten Sachse2

6/5/17

segclassreconstruct --binning_option still works?

Dear David, I believe what probably happened is that the online documentation is ahead of the latest

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segclassreconstruct --binning_option still works?

Dear David, I believe what probably happened is that the online documentation is ahead of the latest

6/5/17

David Hoover, Carsten Sachse5

5/2/17

Slurm, cgroups, and emspring

Dear David, Indeed, this is just noise as it is printed from the GUI when the running directory has

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Slurm, cgroups, and emspring

Dear David, Indeed, this is just noise as it is printed from the GUI when the running directory has

5/2/17

Natalia Pakharukova, Carsten Sachse6

5/2/17

Installation of spring on Ubuntu 16.10

Dear Natalia, It seems that the latest Ubuntu does not have the option of installing libpng12 The

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Installation of spring on Ubuntu 16.10

Dear Natalia, It seems that the latest Ubuntu does not have the option of installing libpng12 The

5/2/17

Andrew Kehr, Carsten Sachse6

4/27/17

AttributeError: 'NoneType' object has no attribute 'copy'

Hi Andy, Thanks for resolving the issue on the list. Best wishes, Carsten On Wednesday, 26 April 2017

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AttributeError: 'NoneType' object has no attribute 'copy'

Hi Andy, Thanks for resolving the issue on the list. Best wishes, Carsten On Wednesday, 26 April 2017

4/27/17

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