on Rwork and Rfree

From: Dialing Pretty
Date: 7 February 2012 08:31

Dear All,

 

After we refine the structure of the protein to satisfactory with satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree always increases slightly after the water picking refinment.

 

Do you have nay idea to solve this problem or any comment?

 

Cheers,

 

Dialing

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From: Eleanor Dodson

Well - it shouldnt!

 Check if there is some problem..
Eleanor

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From: Robbie Joosten

Hi Dialing,

 

Most water picking tools are rather overenthusiastic and end up placing some waters at places where they should not be. This causes some overfitting and an increase of R-free. I'm hideously old-fashioned and recommend conservatively building waters by hand.

There are some good validation tools that help get rid of excess water: centrifuge in PDB_REDO does the basic work; "check/delete waters" in Coot highlights other suspicious waters; WHAT_CHECK checks hydrogen bonding thoroughly, finds nonsense clusters of water and also finds possible ions. It must be noted that all these tools break down at very high resolution where you may get alternate waters. Fortunately, this problem doesn't occur very often.

 

Cheers,

Robbie

 

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From: Pavel Afonine


Dialing,

Just a reminder: there is phenixbb mailing list for Phenix related questions.

Replying to your post: phenix.refine uses very sophisticated criteria for water update (which doen't mean there is no room for further improvement of course). If you believe it placed or removed a wrong water please submit a bug report to me that should include:

1) all input files (reflection data, PDB file with the model, CIF ligand and parameter files if any);

2) the command you used to run the program;

3) explain which waters you believe are wrong.

Pavel.