Hi Petr,
The automatic weighting scheme in the recent Refmac version that comes with
6.2.0 is fine but there is a limit to what it can do if something is seriously
wrong with the model/data/whatever. It has just worked well for me in all
respects (Rw/Rf gap, maps quality, FOM, ligands,
all-the-validation-parameters-you-can-think-of ) on 2.2 and 3 A resolution
structures. In earlier versions (I can't recall how far back) I remember having
to disable the automatic weighting and use my own values. There must be
something else there in the refmac run.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [email protected]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[email protected]] on behalf of Petr Leiman
[[email protected]]
Sent: Thursday, December 08, 2011 9:43 PM
To: [email protected]
Subject: Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Dear Tim,
I agree with you completely. The question then becomes why does the automatic
weighting scheme in refmac allow R and R-free to run away from each other by 8%
in a 1.1 A resolution structure?
Petr
On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote:
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> Dear Christopher,
>
> if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be
> looking at an electron density map with strong model bias, i.e. the map
> shows the features of the model and not of the data. Although at 1.1A
> resolution this seems quite unlikely, but that's what might explain this
> great gap between R and Rfree.
>
> Tim
>
> On 12/08/2011 06:36 PM, Christopher Browning wrote:
>> Dear All,
>>
>> Question: Has anybody ever refined the same structure using PHENIX and
>> then tried REFMAC to see what happens?
>>
>> I did and I stumbled on something funny. I'm refining a structure at
>> 1.1A resolution which was solved with Iodine phasing using PHENIX
>> AutoSolve. Got a great map and the structure was built almost
>> completely. I had to build a few residues myself, and using the
>> published sequence, I started filling in the residues, but as I came
>> nearer the N-terminus, it looked like the density did not match residues
>> from the sequence. I kept the residues as in the sequence, but as you
>> can see from the PHENIX refined picture (below is the link) it still
>> looks like the amino acid sequence in the crystal does not match the
>> published protein sequence.
>>
>> Out of interest I refined the same file in REFMAC, and now the electron
>> density is correct, and the sequence of the amino acids in the crystal
>> matches the published sequence (see link for picture below). Not only
>> that..... my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC).
>>
>> I've also refined the occupancies of the iodide, however the the output
>> FO-FC map from PHENIX complains and the REFMAC map is fine.....
>>
>> How can this be and what causes this?
>>
>> Link for the pictures:
>> Both maps are at identical Sigma levels in both pictures.
>> PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png
>> REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png
>>
>> Cheers,
>>
>> Chris Browning
>>
>>
>>
>
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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