[cctbxbb] Quick start info?

Nathaniel Echols nechols at lbl.gov
Sat Sep 8 16:21:54 PDT 2012


On Sat, Sep 8, 2012 at 3:57 PM,  <esserlo at helix.nih.gov> wrote:
>   this is a question about how to get started quickly. I have looked at the
> sourceforge site for cctbx and read diverse documents but so far I have not
> found documentation that would help me get started fast. I have a
> crystallographic problem which I can probably program from scratch but then
> again why bother if there is a crystallographic tool box around. But well
> despite all the power in it getting it to work seems a bit daunting. Are
> there really good examples? I did get the "sand box quartz model" script to
> work but this is still far off of what I want to do.

Sadly, the lack of documentation (introductory or otherwise) is one of
the biggest holes in CCTBX right now.  Fixing this is a long-term
project; I've started writing a newsletter article that would cover
the basic concepts, but this is going to take a while (and it's really
going to need to be at least two articles to properly cover
macromolecular applications).  We will also need to add proper
documentation to the code.  The problem, as always, is that writing
documentation competes with writing software, and we're already behind
on writing user documentation for Phenix.

Right now you basically have to learn from context, i.e. by inspecting
the code.  The best places to look for hints on proper usage are in
the "examples" subdirectories of each top-level model (cctbx, iotbx,
mmtbx, etc.), and the "command_line" subdirectories.  If you can give
us some idea what you're trying to do (feel free to email me off-list
if you prefer), we can point you to specific scripts.

(A more specific comment on setting up the toolbox: to get to the
point of writing code as quickly as possible, it's easiest to just
download one of the binary bundles, or even a Phenix installer, and
run "cctbx.python" from there.  But it sounds like you've already made
it past this point.)

-Nat


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