[phenixbb] Header accuracy after only refining ligands

Katherine Sippel katherine.sippel at gmail.com
Mon Aug 25 14:25:44 PDT 2014

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
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