[phenixbb] lastest phenix.refine reproducible problem

周文昌 wenchangyu2006 at gmail.com
Wed May 9 14:14:44 PDT 2012

2012/5/9 Pavel Afonine <pafonine at lbl.gov>

> Wenchang,
>  I had two steps refinement:
>> 1->phenix.refine data.mtz model.pdb xray_data.high_resolution=3
>> fix_rotamers=true strategy=individual+adp+individual_sites+tls
>> 2->phenix.refine data.mtz model-refined.pdb xray_data.high_resolution=3
>>  fix_rotamers=false strategy=none main.number_of_macro_cycles=1
> may I ask why is the step #2 ?

Hi Pavel,
thanks for your consideration.

I may explain what I'm doing from the beginning. I feed my model.pdb into
phenix.refine and do the refinement against different resolution from 2.00
to 3.00. There is a R/R-free value for each refinement. Then in the 2nd
step I refine each model from the former refinement at high resolution
limit 3.00, in order to have meaning comparison on which high resolution
limit could give the best model since in this case all the models are
refined at the same high resolution limit.

>  model-refined.pdb is actually from the 1st step, so in principle the
>> R/R-free values should be the same for 1 and 2. However in my case, I had
>> 0.2506/0.2996 for the 1st step but 0.2503/0.2998 for the second.
> Well, 0.2506/0.2996 vs 0.2503/0.2998 I would say the same. Ralf made a
> great comment about this sometime ago - if interested search in phenixbb
> archives.

I did a search, by heart, in order to find Ralf's great comment but I did
not find it. Could you send the link if you have a way to find it?

> Something like a tiny rounding while reading out/in makes the scaling to
> take a route to a slightly different minimum and voila - a slightly
> different R. Or that same rounding makes density sampling a tiny bit
> different and here is tiny bit difference. I guess one can imagine a long
> list of such things.

if reading out/in would make the slightly different R, does this mean I
will get another different R if I rerun it again?

>  I use the latest version of phenix, phenix-dev-1009.
> As of today the latest is 1054, so you are 45+ days behind -:)
> Pavel
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