[phenixbb] Header accuracy after only refining ligands
pafonine at lbl.gov
Mon Aug 25 21:44:20 PDT 2014
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
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?
> "Nil illegitimo carborundum"/- /Didactylos
> phenixbb mailing list
> phenixbb at phenix-online.org
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