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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