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Dear Rajesh,
first of all, a model is not "true" or "false", it can only be
"better" or "worse".
The explanation of what you observe depends on what you did:
- - did you use the identical and very same mtz-file as input to all
three scenarios? Some people take the output mtz and use it as input
to the next refinement cycle, which is a very, very, bad thing to do.
- - did you ensure always the same set of reflections was used for Rfree
when switching between programs?
If not, your R/Rfree are meaningless.
It may also be that combining phenix and refmac5 indeed resulted in a
better mode - both programs have some substantial differences in how
they work.
Best,
Tim
On 01/24/2013 11:12 AM, rajesh harijan wrote:
> Dear All,
>
> I am working on a perfectly twinned data in space group P31. when
> I refine this data with phenix refine the R/Rfree is 26.6/29.4 and
> average B-factor is 38.
>
> I did one test now..... I used phenix refined pdb and refine with
> refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64.
>
> Now I used refmac5 refined pdb and refined with phenix again. Now
> R/Rfree is 22.1/24.8 and average B-factor is 56.
>
>
> My question is, why B-factor gone up now and R/Rfree reduced. In
> which refined model should I believe in. If last refined model is
> true then how should I reduce the B-factor?
>
> Thank you Rajesh
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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