[phenixbb] Few questions

john kryst protkryst at gmail.com
Wed Mar 14 23:56:08 PDT 2007

Hi Pavel !!

        Thanks for your answers... I have one more question..

Is it possible to set the maximum B-factor limit  during adp refinement (
like  in CNS... 5-100)

Regarding rmsd question.. after model building and refinement ...i took the
model and ran only xtal_pdbsubmission  in cns. And that gave the difference
rmsds (phenix 0.007   & cns 0.0218) thats why i got confused.

Once again thaks for you inputs


On 3/15/07, Pavel Afonine <PAfonine at 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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