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 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

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb

-- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Mengbin Chen Department of Chemistry University of Pennsylvania

Got it, thanks Phil! Mengbin Chen On Tue, May 21, 2013 at 4:22 PM, Jeffrey, Philip D. wrote:

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:* [email protected] [ [email protected]] on behalf of Mengbin Chen [ [email protected]] *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 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

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb

-- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Mengbin Chen Department of Chemistry University of Pennsylvania

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Mengbin Chen Department of Chemistry University of Pennsylvania