[cctbxbb] Documentation .... again

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Tue Dec 11 00:44:41 PST 2012

Hi Folks,

I started on something like these for new starters here at Diamond using cctbx - I wrote a couple of very short tutorials focussed around simple tasks. I would post the link however it seems that source forge is having a bad day.

Having these aim to answer a specific use case was helpful, as it did not take so long to write it. I guess we could collate a "cookbook" of these sort of things? That would scale well. I wrote these as latex documents with the code associated with any data - should be trivial to make these into a test case as well. The document describes most of the key bits of the calculation but not necessarily every bit. Happy to post these as examples.

Anyhow happy to help with the effort. A comment I would make is it is also helpful to have someone other than the author "debug" the tutorials...



On 10 Dec 2012, at 22:52, Pavel Afonine wrote:

> 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 tutorial!).
> 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 ?
> Pavel
> 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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