[cctbxbb] Documentation .... again

Pavel Afonine pafonine at lbl.gov
Fri Dec 7 12:41:28 PST 2012

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.


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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