In the section that looks like this in the header of the PDB file out of phenix.refine:

REMARK   3  DEVIATIONS FROM IDEAL VALUES.

REMARK   3                 RMSD     MAX  COUNT

REMARK   3   BOND      :  0.002   0.058   6768

REMARK   3   ANGLE     :  0.634   9.630   9127

REMARK   3   CHIRALITY :  0.046   0.300   1037

REMARK   3   PLANARITY :  0.003   0.040   1182

REMARK   3   DIHEDRAL  : 13.422  88.272   2558

The bottom line is that the PDB file out of refinement contains much of the info you will need for the refinement section of PDB deposition.

Phil Jeffrey 

Princeton

---

From: phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Mengbin Chen [mengbinc@sas.upenn.edu]
Sent: Tuesday, May 21, 2013 4:15 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] depositing pdb files

I see, thanks a lot! Also, where can I get the rmsd dihedral angle value?

Thanks again,

Mengbin

On Tue, May 21, 2013 at 3:56 PM, Ed Pozharski <epozh001@umaryland.edu> wrote:

Just do not report luzzati errors, they are essentially meaningless.  PDB is not going to reject your deposition because of that.

On 05/21/2013 03:15 PM, Mengbin Chen wrote:

Hi Phenix Users,

I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound.  Any suggestions would be appreciated!

Thank you in advance,

Mengbin

--
Mengbin Chen

Department of Chemistry

University of Pennsylvania

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Mengbin Chen

Department of Chemistry

University of Pennsylvania

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