[phenixbb] problem on phenix refine 2

Pavel Afonine pafonine at lbl.gov
Fri Jul 20 22:10:55 PDT 2012


Hi Tong,

I replied to your email yesterday. Did you get it? Just in case below is 
a verbatim copy of my yesterday's reply to you:

****
Hi ??,

hm, this shouldn't normally happen! Could you please send me relevant 
inputs so I can reproduce the problem and see what exactly is happening? 
Also explain how you run autobuild and then phenix.refine.

Pavel

On 7/20/12 5:43 AM, ?? wrote:
> Hi all:
> I do not know if someone mentioned this problem here before. Recently 
> I ran the AutoBuild to build the structure model, and it outputs a 
> best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix 
> Refine using the .pdb and .mtz generated by AutoBuild. The R value 
> increased to 0.23/0.30 by the end of this refine.
> I wonder why this happened? Or if I have done something wrong?
****

Pavel

On 7/20/12 6:56 PM, herohonan wrote:
> Hi all:
> I do not know if someone mentioned this problem here before. Recently 
> I ran the AutoBuild to build the structure model, and it outputs a 
> best model(R/Rfree 0.20/0.24). After that, I tried the program Phenix 
> Refine using the .pdb and .mtz generated by AutoBuild. The R value 
> increased to 0.23/0.30 by the end of this refine.
> I wonder why this happened? Or if I have done something wrong?
>
> (After AutoBuild, I modified the structure and added the substrate 
> moleculars into the structure by hand.
> I thought the increase of the R value was resulted from the inapposite 
> position of the substrates.
> But the R value still increased when I ran the Phenix Refine just by 
> inputting the output of the AutoBuild without any manual modification.)
>
> --
> Tong Huo
> Ph.D candidate
> College of Life Sciences
> Nankai University
> Tianjin, China
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb


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