On 3/15/07, Pavel Afonine <PAfonine@lbl.gov > wrote:

Hi John,

thanks for you question!

> 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.

No, phenix.refine does not create the deposition ready PDB file header.
However, there are lots of information in the PDB file header so you can
extract it and format the way you want.

> 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.

This is a question for Tom Terwilliger. I hope he will answer it.

> Does the rmsd estimation (for eg. rmsd_bonds ) depends on the program
> we use ??

Different programs use different dictionaries for the standard geometry,
so it's not surprising the migrating from one program to another you get
slightly different values.

Also, it is important to look at the values at right moment: for example
if CNS gave you 0.0218 A but phenix.refine says it it 0.007A, to me it
looks like phenix.refine already did some refinement and as result the
values are not really comparable.

Please, let me know you still have questions!
Pavel.
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