What about some wiki format? :)<br clear="all"><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)"><p><font face="arial, helvetica, sans-serif">Claudia Millán (<a href="mailto:cmncri@ibmb.csic.es" style="color:rgb(17,85,204)" target="_blank">cmncri@ibmb.csic.es</a>)</font></p>
<p><font face="arial, helvetica, sans-serif">Institut de Biologia Molecular de Barcelona (IBMB-CSIC)</font></p><p><font face="arial, helvetica, sans-serif">Barcelona, Spain</font></p></span></div><br>
<br><br><div class="gmail_quote">2012/12/7 Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>These are basic parameters for FFT
based Fcalc calculation.<br>
<br>
algorithm = fft or direct summation<br>
wing_cutoff - is how far away from atomic center you sample
density around atom;<br>
u_base (or b_base) - is additional smearing B-factor if input atom
has too small B so it falls between the grid nodes;<br>
quality_factor - determines accuracy of sampled density.<br>
<br>
For s review, see:<br>
<br>
Acta Cryst. (2004). A60, 19-32 <br>
On a fast calculation of structure factors at a subatomic
resolution<br>
P. V. Afonine and A. Urzhumtsev<br>
<br>
and references therein.<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
<br>
On 12/7/12 12:35 PM, Richard Gildea wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">Hi Graeme,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>As to your specific question:</div>
<div><br>
</div>
<div>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: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448510/" target="_blank">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448510/</a></div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Richard</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 7 December 2012 01:59, <span dir="ltr"><<a href="mailto:Graeme.Winter@diamond.ac.uk" target="_blank">Graeme.Winter@diamond.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="blue" vlink="purple" lang="EN-GB">
<div>
<p class="MsoNormal">Hi Folks,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">cctbx_project/cctbx/xray/structure.py</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">…</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> def structure_factors(self,
anomalous_flag=None, d_min=None,</p>
<p class="MsoNormal">
algorithm=None,</p>
<p class="MsoNormal">
cos_sin_table=False,</p>
<p class="MsoNormal">
quality_factor=None,</p>
<p class="MsoNormal">
u_base=None,</p>
<p class="MsoNormal">
b_base=None,</p>
<p class="MsoNormal">
wing_cutoff=None):</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">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?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I would be happy to help with this,
though the above example is not one where I know the
answer!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Thoughts?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Best wishes,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Graeme</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dr.
Graeme Winter</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Senior
Software Scientist</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Diamond
Light Source</span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><a href="tel:%2B44%201235%20778091" value="+441235778091" target="_blank">+44 1235
778091</a> (work)</span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><a href="tel:%2B44%207786%20662784" value="+447786662784" target="_blank">+44 7786
662784</a> (work mobile)</span><span></span></p>
<span><font color="#888888">
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
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