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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md index 8dee0a28..9e5490c9 100644 --- a/2021/talks/molecular.md +++ b/2021/talks/molecular.md @@ -8,8 +8,6 @@ # Reproducible molecular graphics with Org-mode Blaine Mooers - - [[!inline pages="internal(2021/info/molecular-schedule)" raw="yes"]] Research papers in structural biology should include the code used to make @@ -48,6 +46,37 @@ 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? |