Tutorials: Getting started with HTMD, Playing with HTMD Molecules and Atom Selections

[j3mdamas]

I am going through the tutorials and fixing them.

I think that the "Getting started with HTMD" tutorial [1] and the "Playing with HTMD Molecules" tutorial [2] strongly overlap and could be condensed into only one tutorial called "Getting started with HTMD Molecules", where the Molecule class and its features are introduced.

Furthermore, the "Atom selections" tutorial [3], where @tonigi did an awesome job, is actually more like a documentation page rather than a tutorial. My idea would be to use this material intercalated with snippets of code to take advantage of the notebook capabilities. @giadefa told me this was created as a presentation, but I don't it will lose its purpose as that.

Task list:

• get rid of redundancies in the first two tutorials
• create a new tutorial which is a fusion of tutorials [1] and [2]
• incorporate the tutorial [3] into the new tutorial, making an extended and dedicated overview of the Molecule class, selection capabilities, features and methods (postponed)

[j3mdamas]

First point done.
Tutorial [1] cleaned and small formatting/bug solved. Commit: j3mdamas/htmd@a1ca92c002dd01fca840a1dca5ea33fd3bc55ec6
Tutorial [2] also cleaned and reformatted. Some parts of tutorial [2] were removed because they were redundant with tutorial [1]. A small section on Molecule.insert was moved from [2] to the appropriate part in [1]. I did not test the trajectories section, I did not have one to test. Commit: j3mdamas/htmd@f89e372b32884a1e0375b586cbe1216be373f386

Second point is ongoing. @giadefa, it may not be ready for Thursday, but we'll see.

[j3mdamas]

Second point done. Commit: j3mdamas/htmd@18a91da930ed26270d0fb685e10c8a8017cdbbe8
More redundancies were removed. The tutorial is also Slide-mode ready. It's a bit clunky in that mode, because of a RISE issue (damianavila/RISE#188), but it works.

@giadefa is possibly going to use it on the Masters classes tomorrow, and if he thinks its OK, it may replace tutorials [1] and [2] in the future.

EDIT: the trajectory section is now tested too.

[j3mdamas]

I think the new tutorial was adopted. Tutorials [1] and [2] deleted. Point 3 postponed.
Commit: j3mdamas/htmd@701f4ac81af59bafb0b52fc971913a3e62e85e7a
Issue closed.

[stefdoerr]

Beyond adopting it we should also put it online no? :D So I guess we should pull it to the multiscalelab fork and then make a new doc publishing

[stefdoerr]

@giadefa I guess we need to first do a pull request from @j3mdamas fork into acellera and then pull from the acellera repo into our multiscalelab fork. Can you do it?

[j3mdamas]

Gianni already did it, but using my file directly instead of pulling from
my branch. It's alright but I'll need to fix the website because it's buggy
on the menus.
On Apr 14, 2016 6:45 PM, "Stefan" notifications@github.com wrote:

@giadefa https://github.com/giadefa I guess we need to first do a pull
request from @j3mdamas https://github.com/j3mdamas fork into acellera
and then pull from the acellera repo into our multiscalelab fork. Can you
do it?

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