[cctbxbb] Documentation .... again

Mon Dec 10 00:35:39 PST 2012

To be honest I would say simply adding it to the code would work better as it's easier to maintain and makes it available to libtbx.help. Once you have a wiki you have something extra to do when you make changes to code, to see if the wiki needs updating.

That said, a *separate* wiki with more of a how-to feel could be useful, however this has been mooted several times and not happened, I think because the activation energy is not trivial. The main resource - volunteers with useful knowledge and spare time - is in rather short supply.

Just MHO,

Cheerio,

Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Claudia Millán Nebot
Sent: 10 December 2012 08:31
To: cctbx mailing list
Subject: Re: [cctbxbb] Documentation .... again

What about some wiki format? :)

Claudia Millán (cmncri at ibmb.csic.es<mailto:cmncri at ibmb.csic.es>)

Institut de Biologia Molecular de Barcelona (IBMB-CSIC)

Barcelona, Spain

2012/12/7 Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>>
These are basic parameters for FFT based Fcalc calculation.

algorithm = fft or direct summation
wing_cutoff - is how far away from atomic center you sample density around atom;
u_base (or b_base) - is additional smearing B-factor if input atom has too small B so it falls between the grid nodes;
quality_factor - determines accuracy of sampled density.

For s review, see:

Acta Cryst. (2004). A60, 19-32
On a fast calculation of structure factors at a subatomic resolution
P. V. Afonine and A. Urzhumtsev

and references therein.

Pavel

On 12/7/12 12:35 PM, Richard Gildea wrote:
Hi Graeme,

I agree that the documentation of much of the cctbx code is somewhat lacking, although I am not sure what is the best solution (especially for the huge volumes of code that is already written). Perhaps some combination of people adding documentation when asking or answering questions on here about specifics would go some way to helping future users of the code.

As to your specific question:

Setting cos_sin_table=True uses interpolation of values from a pre-calculated lookup table for trigonometric function calls in the structure factor calculations in preference to calling the system libraries. Ralf makes some comment on the speed (and variation in speed) of the trigonometric functions in system math libraries in his FABLE paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448510/

However, without digging into the source, I am not sure of the meaning of some of the other keywords to that function (e.g. wing_cutoff), which makes it hard for me to write comprehensive documentation for this class.

Cheers,

Richard

On 7 December 2012 01:59, <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
Hi Folks,

Been thinking some more about the old chestnut of documentation. The lack thereof is a well understood issue, and to be honest one which is not going to change any time soon as no one has the time to maintain a manual - this is fine and well understood.

As a kind of "patch" for this I was wondering if it would be possible to have a forum where someone could ask for e.g. documentation for a currently undocumented function, which could then be added to the subversion in the code itself. For example:

cctbx_project/cctbx/xray/structure.py

...

  def structure_factors(self, anomalous_flag=None, d_min=None,
                              algorithm=None,
                              cos_sin_table=False,
                              quality_factor=None,
                              u_base=None,
                              b_base=None,
                              wing_cutoff=None):

what is cos_sin_table for? with things like this there is the attitude that it is safe to ignore, however if we're writing code to guide people's experiments it would be good to be sure of this. Some simple documentation explaining this would be very useful.

I'm definitely not suggesting (i) that anyone writes a manual or (ii) that all undocumented functions are suddenly documented, only that there is a mechanism set up that someone could ask about this and that someone who knows the answer could commit the changes to cctbx and then reply with the diffs - perhaps the way that stackoverflow works, or an email, or something really lightweight. Even this mailing list could be used I guess?

I would be happy to help with this, though the above example is not one where I know the answer!

Thoughts?

Best wishes,

Graeme

Dr. Graeme Winter
Senior Software Scientist
Diamond Light Source

+44 1235 778091<tel:%2B44%201235%20778091> (work)
+44 7786 662784<tel:%2B44%207786%20662784> (work mobile)

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