Informal EMAN2 Python group - invitation

[Ludtke, Steven J.]

Weekly on Thursdays from Noon - 1 or 2 PM (US central time, use Houston or Chicago in a calendar). 

Targeted at about an hour, but may continue for up to 2 hours depending on what we're doing. 

https://bcm.zoom.us/j/98285850226?pwd=NWJydlJKREdBYWs3SEk5TGZoV3MvZz09

A few weeks ago I started running a weekly discussion session for people in my group and a few other groups at BCM to discuss using EMAN2 from Python, both via the new Jupyter Lab tools and writing standalone python scripts. The first few meetings we focused on how to write GUI programs, and as a group we put together a simple GUI program for displaying simultaneous projections of multiple maps:

examples/e2compare_projections.py

Anyway, I thought I would open the meeting up to other people who might be interested in using EMAN2 from Python. This is an informal discussion group rather than a didactic course, so our topics will meander from week to week depending on what people want to learn either for specific projects or their own curiosity. We have been moving to integrate EMAN2 tools more closely with the NumPy & Tensorflow ecosystems making it useful for a wide range of structural biology tasks and interfacing with deep learning code. 

We have started doing some of these in person again, but I will also run a Zoom meeting for each, in case anyone is interested:

https://bcm.zoom.us/j/98285850226?pwd=NWJydlJKREdBYWs3SEk5TGZoV3MvZz09

feel free to join in and just speak up if you have any questions/comments. Today we are going to generate some helices and discuss some concepts around finding them in tomograms (we started on this last week, but didn't actually "do" much of anything). 

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

[Colin Gauvin]

This sounds fantastic, I didn't see it in time for today but will add it to my calendar and attend next week. I have been tinkering around trying to solve some esoteric problems so this could not be better timing. Thanks for opening this up.

[Ludtke, Steven J.]

For any who plan to join consistently, if you send me a direct email, I will add you to the email group for the meeting. 

I'm attaching the small Jupyter lab notebook from today's session to this message to give you an idea of some of the sorts of things we might discuss. Note that to use this you must have a pretty up to date EMAN2 install (not the year+ old 2.91 release), and you need to run 

e2display.py --server

before using the e3display commands in the notebook. Just run 'e2.py' from the folder containing the notebook and you should be able to open it from there.

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

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