amber-developers: please proofread and update the Amber 10 documentation

From: David A. Case <>
Date: Sat, 2 Feb 2008 21:27:54 -0800

Hi everyone:

Amber serves a big community of users, not the least of which are new people
that come into our labs with no detailed background in Amber. So it helps us
and everyone to have good documentation, and it needs to be prepared as
carefully as the code itself.

Please, please, take some time an examine the following:

    amber10/doc/AmberTools.{lyx,pdf} and amber10/doc/Amber10.{lyx,pdf}

a. check for correctness and completeness; remove obsolete material; add
   examples whereever anything might be ambiguous. Add references
   to the appropriate test cases if that would help show how things are done.

   [Because of the move to LyX/latex, there may be real glitches and
   conversion errors that need to be corrected. But view this as an
   opportunity for general updates as well.]

b. Update the literature references! Many of these are to *your* work, and
   the Amber manual is one way that people will find your papers and take
   advantage of them. Yet most references are still unchanged from Amber 9,
   and hence are at least two years old.

You will see that the manuals have been extensively reorganized recently. I
hope this all make sense, but I welcome suggestions or contributions that are
"big" changes (i.e. more than just proofreading corrections.) How can we best
aid both experts and relatively new people?

Please remember that there is a lead time to get manuals run off and bound:
updates to the manuals need to be made a soon as possible.

I've put in lots of hours to get us as far as we are now, and am feeling
grumpy that I haven't had more help. (Some of you have been good about this,
and I appreciate this.) Consider assigning each person in your group 10 pages
or so, and ask them to do a careful reading, with a one-week deadline for
getting back to you. Or an updating party with beer and pizza. Or whatever
makes sense, but let's try to spread the work out and get as many people as
possible to contribute.

Received on Sun Feb 03 2008 - 06:07:44 PST
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