Re: [AMBER-Developers] Tutorials

From: Jason Swails <>
Date: Wed, 28 Sep 2016 22:42:35 -0400


> On Sep 28, 2016, at 7:20 PM, David Cerutti <> wrote:
> I've mirrored the new site here:

It's not clear to me that this is an improvement. To start with, there is at least one tutorial missing from the table of contents (the constant ph one). Not sure if there are more.

The numbering scheme is also haphazard and confusing (the links don't have to match the names).

Lastly, having everything on the same page makes it easier to search with little things like searching for text. It also removes the need to keep tutorials listed and updated in 2 places (the ToC and the other pages they belong in), making it easier to maintain and less likely to fall out of sync (and become even more confusing).

On the whole, I liked the last layout more. Also, the change *to* that layout followed a lengthy conversation (and it was within the past few years). I think this change should be reversed in master for now and discuss some before such changes are made.

All the best,

> The front page looks as intended, but I've done some things to a special
> tutorials.css style sheet that break the captions in some of the
> descriptions if you peruse the various sections (some tutorials' ToC
> graphics are a lot bigger than 128 x 128). The reason for this change was
> that there are some really pretty images in there that don't show up well,
> and I want people to be able to make images with a size that suits them for
> their ToC blurb. I've more or less fixed all of the pages except for Dan's
> CPPTraj examples. However, if anyone can help me fix this business about
> images over-running the boxes around each ToC item, that would be very
> helpful. See, for example:
> If we can fix that over-running problem then all of the tutorials will get
> a fair shake and future contributors will have good artistic license.
> Dave
> On Wed, Sep 28, 2016 at 5:14 PM, Jason Swails <>
> wrote:
>> On Wed, Sep 28, 2016 at 5:00 PM, David Cerutti <>
>> wrote:
>>> This is what I was asking Dave earlier; I was under the impression that,
>>> like the software, there is a moderation process and so things that get
>>> pushed to master are NOT world-viewable until they graduate from the
>> master
>>> branch to the directories actually on , but apparently I am
>>> mistaken and anyone with write access to amber_web can change the webpage
>>> at will.
>> Sort of. The 'upstream' repository is not the live website, but the live
>> website pulls from it.
>> But it's inconvenient for most people to do real-world testing on a
>> proposed change without making the webpage live (most people won't be able
>> to look at it until it goes live).
>> So don't make any changes to the master branch that you don't intend to go
>> live immediately as a general rule of thumb.
>> All the best,
>> Jason
>> --
>> Jason M. Swails
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>> AMBER-Developers mailing list
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Received on Wed Sep 28 2016 - 20:00:03 PDT
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