Repository for Jupyter notebook sessions with EMAN2 demos/docs

[Ludtke, Steven J.]

Good suggestion Muyuan, to use GitHub for Jupyter notebooks for documentation/example purposes. They are presented well directly on the site, and as you say, they are reasonably sized. However, I prefer to keep them separate from the main EMAN2 distribution for several reasons (users only installing the binary can still get them easily, fewer triggers to rebuild EMAN2, etc.). So, I created an official repository for these. I would suggest that we come up with some sensible naming strategy. Maybe topical folders?  If this catches on, we don't really want one folder with a hundred notebooks in it.  Anyway, please feel free to commit useful things here:

https://github.com/cryoem/eman2-jupyter

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

[Thorsten Wagner]

Hi,

when I try to use "Save Box Coord" in the e2spt_boxer.py I get the following exception:

Traceback (most recent call last):                                                                                                                                                                                                                                             
  File "/home/twagner/Applications/miniconda3/envs/sphire_py3/bin/e2spt_boxer.py", line 513, in menu_file_save_boxloc                                                                                                                                                          
    out=file(fsp,"w")                                                                                                                                                                                                                                                          
NameError: name 'file' is not defined                                                                                                                                                                                                                                          
Aborted (core dumped) 

Seems to be Python3 related. Changing it from file() to open() fixes that issue.

Best,

Thorsten

_____________________________

Dr. Thorsten Wagner

Max-Planck-Institute of Molecular Physiology

Structural Biochemistry

Otto-Hahn Strasse 11

D-44227 Dortmund

Phone +49-(0)231-133-2357

PGP Key ID: 6BDBA8FA7FDA6CE3

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Von: eman2-de...@googlegroups.com <eman2-de...@googlegroups.com> im Auftrag von Ludtke, Steven J. <slu...@bcm.edu>
Gesendet: Sonntag, 30. August 2020 15:44
An: Chen, Muyuan
Cc: eman2-de...@googlegroups.com
Betreff: [eman2-developers] Repository for Jupyter notebook sessions with EMAN2 demos/docs

 

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