[ccp4bb] on Rwork and Rfree

2012-02-07 Thread Dialing Pretty 
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

Re: [ccp4bb] on Rwork and Rfree

2012-02-07 Thread Eleanor Dodson 

On 02/07/2012 08:31 AM, Dialing Pretty wrote:

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



Well - it shouldnt!

 Check if there is some problem..
Eleanor

Re: [ccp4bb] on Rwork and Rfree

2012-02-07 Thread 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

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Dialing Pretty
Sent: Tuesday, February 07, 2012 09:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] on Rwork and Rfree

 

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

Re: [ccp4bb] on Rwork and Rfree

2012-02-07 Thread Pavel Afonine 
Dialing,


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?


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.