[phenixbb] Third issue (...) - P.S.

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Mon Aug 1 02:03:00 PDT 2011

Thanks for the elaboration.  All I meant was that figure 2 did not show 
improvements (points pretty much on the y=x line), while figure 1 showed 
huge improvements (points below the y=x line).  I should have added that 
in the past I've had puzzled questions around here about phenix results 
at lower resolutions, and I always wondered whether weight optimization 
may be an issue.

So maybe what I was looking for was a figure like figure 2, but of the 
old optimization.


On 29/07/2011 17:41, Pavel Afonine wrote:
> Hi Frank,
> thanks for prompting me to have another look at this! Yes, a quick
> section reiterating the results shown in both figures would be
> definitely helpful. Ok, I'm doing it now (better late than never!):
> Figure 1 (old version vs new version), going from left to right, top to
> bottom:
> - the new procedure always produces smaller Rfree-Rwork gap (except two
> outliers out of ~110 cases). In a few dozens cases this means going from
> Rfree-Rwork ~10-14% down to 8% and less. Which is I believe an improvement.
> - Molprobity clashscore gets much lower in all cases, and in many cases
> it get down from clashscore>150-200 to less than 50. Again, I take this
> as an improvement.
> - Ramachandran plot: always less outliers, and in a few dozens cases it
> get down from 10-25% to less than 5%. It's good too!
> - Always less Rotamer outliers. Not bad.
> -<Bij>  for bonded atoms gets always smaller. In many cases it goes down
> from ridiculously high ~30-50A**2 to less than 20 or so. There are
> outliers which, as pointed out in the text, need investigation.
> - Rfree difference wise (the last graphic at the bottom), almost all the
> differences stay within "equally good range of values", which is defined
> in the text. Some bad outliers, are 1) inoptimal NCS groups selection
> (which was done automatically using the old procedure, not the new one
> that does it in torsion angle space), 2) not using TLS even though this
> was used originally, and other issues that needs an investigation. There
> are improvements too.
> Figure 2 (with weight optimization vs without weight optimization):
> going from left to right, top to bottom:
> - Rfree-Rfree gets much better in a few dozens of cases, or stays in a
> "equally good range of values".
> - clashscore either stays the same or gets smaller, which is good. Same
> for Ramachandran and Rotamer outliers.
> - Except two outliers (out of total ~110 cases), Rfree(opt)-Rfree(no
> opt) is consistently smaller, with a number of cases having significant
> improvement (over ~2% or so).
> Thanks again for your comments, and prompting me to spell out a proper
> analysis of the presented pictures.
> Pavel.
> On 7/29/11 1:21 AM, Frank von Delft wrote:
>> Hi, just scanned through the article on automatic weight adjustment.
>> If I had to summarise figures 1 and 2, I'd have to conclude that the
>> latest weight optimization only occasionally produces better results
>> than not doing it (fig 2);  and that therefore the old optimization
>> was considerably worse than doing nothing at all.
>> Or have I misinterpreted it?
>> Cheers
>> phx
>> On 28/07/2011 19:59, Nigel Moriarty wrote:
>>> Dear Colleagues,
>>> I am pleased to announce the publication of the third issue of the
>>> Computational Crystallography Newsletter:
>>>          http://www.phenix-online.org/newsletter/
>>> A listing of the articles and short communications is given below.
>>> Please note that the newsletter accepts articles of a general nature
>>> of interest to all crystallographers. Please send any articles to me
>>> at
>>> NWMoriarty at lbl.gov noting that there is a Word Template on the website
>>> to streamline production.
>>> Articles
>>> --------
>>> Improved target weight optimization in phenix.refine
>>> Mite-y lysozyme crystal and structure
>>> Short communications
>>> --------------------
>>> A lightweight, versatile framework for visualizing reciprocal-space data
>>> An extremely fast spotfinder for real-time beamline applications
>>> Hints for running phenix.mr_rosetta
>>> Cheers
>>> Nigel
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