Re: [phenixbb] refinement with anomalous data

6 Feb 2015

      Once again, you cannot compare R factors calculated using different sets 
of data.
Pavel

On 2/6/15 11:48 AM, Guangyu Zhu wrote:
...
That’s how I think. But say if I+ is exactly same as I-, I use it 
twice. I got much lower R and Rfree, that means better fit. Isn’t 
good? And I’m also curious why.
Guangyu
From: Pavel Afonine mailto:[email protected]>
Date: Friday, February 6, 2015 at 2:29 PM
To: Guangyu Zhu mailto:[email protected]>, 
"[email protected] mailto:[email protected]" 
mailto:[email protected]>
Subject: Re: [phenixbb] refinement with anomalous data
If data set isn't anomalous then I don't see why you would want to 
refine against I+/I-.
Pavel
On 2/6/15 11:26 AM, Guangyu Zhu wrote:
...
What I meant is: I actually don’t have anomalous signal, so when I 
use I+/I-, kind of like I use Imean twice for each reflection. Can I 
do that?  My guess is that the resolution is low, so double 
reflection/parameter ratio really benefits the refinement, although 
overall the weight for x-ray term is not change, because rms bond and 
angle are similar.
Newer versions are better for my other refinement with higher 
resolution, but not this data set.
Guangyu
From: Pavel Afonine mailto:[email protected]>
Date: Friday, February 6, 2015 at 2:12 PM
To: Guangyu Zhu mailto:[email protected]>, 
"[email protected] mailto:[email protected]" 
mailto:[email protected]>
Subject: Re: [phenixbb] refinement with anomalous data
...
I use same data set for refinement, so Rfree is also marked for same 
reflection. The only difference is that I chose “Data labels” from 
Phenix IMEAN or I(+) I(-).
What I meant is that the IMEAN set is not the same as I(+),I(-) at 
least because the number of reflections in IMEAN is not the same as 
in I(+),I(-).
...
By the way, I use version 1.8.2 for refinement. Newer versions gives 
higher R/Rfree.
Should be the other way around...
Pavel