[phenixbb] Header accuracy after only refining ligands

Pavel Afonine pafonine at lbl.gov
Mon Aug 25 21:44:20 PDT 2014

Hi Katherine,

you can take RMSD from PDB file header, example:

REMARK Final: r_work = 0.1588 r_free = 0.1773 *bonds = 0.015 angles = 1.221*

or if you scroll down some more:

REMARK   3                 RMSD     MAX  COUNT
*REMARK   3   BOND      :  0.015   0.620   4192**
**REMARK   3   ANGLE     :  1.221   7.451   5663**
or from phenix.refine log file.

Also you can just calculate them from PDB file:

phenix.pdbtools model.pdb model_stat=true


On 8/25/14 2:25 PM, Katherine Sippel wrote:
> Hi all,
> I was trying to prep a structure for PDB deposition. All the protein 
> atoms were good, but I needed to correct some ADP and ligand issues. I 
> ran coordinate refinement only on the ligands and subsequent ADP 
> refinement. Everything was good, except the RSMD values output are 
> clearly only for the ligands. Now I am wondering which values in the 
> header I can trust as far as deposition goes. I tried to do a 
> workaround where I ran refine with 0 macrocycles to see if I could get 
> the proper values, but obviously the bulk solvent is different and I 
> get higher R values.
> I am wondering if I can run validation to get the correct RMSD values 
> or if there are other header values that might have been affected by 
> not refining all the coordinates?
> Cheers,
> Katherine
> -- 
> "Nil illegitimo carborundum"/- /Didactylos
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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