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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md index b2ebfaa4..3cc7d829 100644 --- a/2021/talks/molecular.md +++ b/2021/talks/molecular.md @@ -8,7 +8,7 @@ # Reproducible molecular graphics with Org-mode Blaine Mooers - +[[!taglink CategoryOrgMode]] [[!inline pages="internal(2021/info/molecular-schedule)" raw="yes"]] @@ -48,6 +48,61 @@ from Org-mode documents. # Discussion +Pad: + +- Q1: Do you also do any hydrogen-bond analysis in your workflows? + Also, could your snippet library be extended for other non-python + simulation programs like GROMAC? + - A: Yes, i have a snippet that generate publication qualtiy + hydrogen bonds. Yes, I have thought of making snippet library + molecular simulation like Gromacs and AMNER and drug design + software packages like autodock Vvna and rdkit. They can help + lower the barrier to entry. I made library for crystallographic + computing with CCTBX for use in Jupyter. I should make it + available for org-mode. +- Q2: We've seen a few talks regarding managing academic papers and + citations in emacs/org, what does your workflow look like? + - A: I switched to Emacs as my primary editor 3 months ago. I have + yet to write a paper in Org. I am very comfortable with LaTeX + and I have been writing my papers on Overleaf in LaTeX for + several years. I used bibtex and JabRef to manage by refernces. + I have started playing by org-ref. It looks super promising. +- Q3: Hi Blain, you mentioned that you have been able to come back to + a file years later, how do you manage the environment that the org + file executes in? + - A: Good question. The PyMOL code is good for years so the images + should be reproducible regardless of the version of org. + PyMOL's domain specific language is very stable. The Python + code largely just wraps around the DSL code. +- Q4: Have you used Org Mode and pyMOL for publications? Could you + share a link to any of them? + - A: I have yet to use org in a publication. The first step will + be to use it for supplemental material. + +BBB discussion: + +- We've seen a few talks regarding managing academic papers and citations in emacs/org, what does your workflow look like? + - Blaine: My workflow involves a dozen different software packages and 20-200 GB of data. Complete literate programming is not possible at this time. The smallest possible step towards that goal is to make the molecular images reproducible because the files involved are on 1-100 MB in size. + - Questioner: I assume that's why there might be lag with several images rendered on an org buffer? +- I was specifically interested in your workflow with managing citations and papers as I'm sure you have to do, is there anything in particular you use for citation management? + - Blaine: I switched to Emacs as my primary editor 3 months ago. I have yet to write a paper in Org. I am very comfortable with LaTeX and I have been writing my papers on Overleaf in LaTeX for several years. I used bibtex and JabRef to manage by references. I have started playing by org-ref. It looks super promising. + - Questioner: I still use zotero and biblatex, but the previous two talks about org-ref got me thinking about my workflow +- Have you used Org Mode and pyMOL for publications? Could you share a link to any of them? + - Blaine: I have yet to use org in a publication. The first step will be to use it for supplemental material. + - thanks, makes sense, I'm off in a part of the python world where code base churn can be pretty severe; but it sounds like pymol is able to avoid those issues + - Blaine: PyMOL as a domain specific language that is very stable. The transition from Python2 to Python3 as bit disruptive. +- Hi Blaine, you mentioned that you have been able to come back to a file years later, how do you manage the environment that the org file executes in? + - Blaine: Good question. The PyMOL code is good for years so the images should be reproducible regardless of the version of org. + +BBB feedback: + +- Blane, great job with the talk. Awesome presentation. + - I know people loved it in the IRC chat :D +- I can share that I was excited to see how you made things so seamless and integrated feeling into Emacs. The results are really eyepopping. + + +IRC discussion: + - which is the package name for export org mode to pymol? - the async header argument can be helpful with the problem of the amount of time for generating the images - think of this is use case explication for being able to manage and render 3d models in org |