Hi Lothar, yes, that's right. Please tell us what exactly you want to do and some one may be able to send you a simple script-example that will do what you want or a similar task. I have gazillions of various "10-liners" that do things from manipulation files to minimization of functions and simple refinements. That may be faster and more efficient than wasting time on writing documentation and (what's most important, hard and tedious!) proper maintaining it. Also, I can name two very good and helpful resources: 1) some trees have "examples" sub-directories, and 2) our standard tests (see tst*.py files in various locations that typically exercise (and therefore exemplify) most of available functionality). Pavel On 9/9/12 7:52 AM, [email protected] wrote:

Dear Dr. Echols,

thanks for the fast reply. So I will study the documentation that is there more carefully and look at the examples in each section. And yes, I downloaded the latest official release for CentOS 5.5 and it runs as far as I can tell just fine under CentOS 6.2

Best regards,

Lothar

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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

On Sat, Sep 8, 2012 at 3:57 PM, wrote: 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.)

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