[phenixbb] Few questions

Hi phenixbb !! I have few questions. 1. Is there any utility in phenix to write out pdb formatted (which is ready to deposit) output file.. like xtal_pdbsubmission utility in CNS. 2. In Autobuild wizard how to ask the program to use the Free R flags present in the file. It always generates new Free R flags during refinement. One general question. Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program we use ?? I have been refining in CNS. then i used Autobuild wizard to build my model. when i went back to cns the rmsd of bond increased (0.0218 A). But phenix.refine says it it 0.007A. Thanks in advance for your kind inputs. regards john