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

Pavel Afonine pafonine at lbl.gov
Fri Jul 29 09:41:56 PDT 2011

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 

- 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.


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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