[cctbxbb] Documentation .... again

Pavel Afonine pafonine at lbl.gov
Mon Dec 10 14:52:26 PST 2012

I've been having this plan too for quite some time, and yes, I've never 
had time to do anything (and most likely wouldn't in near future). 
However doing it collectively may cut on amount of time and effort, thus 
making it practical in the end.

I would plan it first. To start, I would say we need:

1) find out who wants to participate;
2) write a framework and agree on it. I see it as a list of bullet 
points outlining the subjects that we are going to cover.
3) then we see who wants (and can) to cover what and do the first step: 
everybody fills in his/her contribution.
4) then we collectively review the whole thing, and do a few iterations 
of that until we are satisfied with what we have.

Additional thoughts:

I know it may make things slightly more complex, but I suggest that we 
make sure that every example provided in the tutorial is exercised as 
part of our routine tests. This will ensure that the effort we are going 
to invest will not be obsoleted shortly after it's complete. Also, this 
would imply the document may change if a cctbx functionality described 
in it changed (so it's not a static paper). I did this for command line 
version of phenix.refine several years ago, and it seems to work well 
(though I'm not saying that we should do it the same way for this 

I have zero experience with Google Docs, so these couple of questions 
are rather out of my ignorance. Does it allow to 1) insert formulas, 2) 
put pieces of code that can be extracted automatically for exercising ?


On 12/10/12 2:22 PM, Nathaniel Echols wrote:
> On Mon, Dec 10, 2012 at 2:18 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> depending on your vision of this, perhaps such tutorial should be a
>> collective effort between those who would like to volunteer to participate.
>> Also, that may help to cut down your time for preparing it.
> That was indeed the plan, but it's not like anyone else around here
> has more free time.  I'm happy to share the Google Doc of what I've
> written so far if anyone would like to contribute.  (The plan was
> actually to write it in at least two parts: first part would cover
> fundamentals of scitbx and cctbx, part two would cover applications to
> macromolecules, i.e. iotbx.pdb and mmtbx.)
> -Nat
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