Re: [AMBER-Developers] Tutorials, II

From: David Cerutti <dscerutti.gmail.com>
Date: Tue, 4 Oct 2016 11:09:35 -0400

I will correct any titles I changed; the only intention was to make them
shorter if possible to fit in a compact format. I will also do things to
delineate one section from another. Not so visible in the result is that
I've now got .php server-side includes working, so it's very easy to
migrate the format and apply consistency to many pages without ever writing
the same code twice. I will be extending the new format to the other
tutorials pages, and pare down the current set of images while I do it.

On Tue, Oct 4, 2016 at 10:47 AM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Mon, Oct 3, 2016 at 7:27 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
> > How does it look now?
> >
> > http://casegroup.rutgers.edu/~cerutti/amber_web/tutorials/
> >
> > I have the masthead.jpg image rendered with layers in .xcf format (Gnu
> > Image Manipulation Program), anticipating that we can make that our
> banner
> > with a bit of text-as-image. (I'd suggest "AMBER Molecular Simulations,"
> > but I'm sure we'll have some exchanges about the exact words.)
> >
> > I've tried to nail things down pretty well but I haven't yet tested
> across
> > many browsers.
> >
>
> Some added comments: keep the whole original titles of the tutorials. In
> many cases, there is a reason tutorial authors chose what they chose. I'll
> harp again on the constant pH tutorial, since that's one Dwight and I wrote
> and I can only spare quick glances.
>
> The interesting part of that tutorial is learning how to run a constant pH
> calculation. If someone comes to the tutorial page wanting to run constant
> pH, they can search for "cphmd" or "constant pH" or "pH" on the main TOC
> page and not find anything. The tutorial is not there to show people the
> best way to calculate a pKa -- it's there to show them how to run a CpHMD
> simulation.
>
> Having that tutorial titled "Calculating pKas for titratable side chains in
> hen egg white lysozyme" masks the true purpose of that tutorial. I haven't
> checked all the other tutorials to see if similar statements apply to
> those.
>
> Other, more minor comments on aesthetics:
>
> 1. Numbers are better than bullets -- it's easier to reference when asking
> questions or pointing resources out to someone (look at item 3 on page
> www.referencetosomething.org)
> 2. The titles of the tutorial categories are the same font and size as the
> tutorials themselves, making them hard to distinguish.
>
> My suggestion: have the titles be centered over the groups with a larger
> font and enumerate the individual tutorials below them.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
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Received on Tue Oct 04 2016 - 08:30:02 PDT
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