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 DEVIATIONS FROM IDEAL VALUES.
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

Pavel

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
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