[phenixbb] Few questions
emckee at cs.tamu.edu
Thu Mar 15 00:18:19 PDT 2007
i believe that is refinement.adp_restraints_iso.b_iso_max that you wish to
set.... I don't think there is a min, though...
On Thu, 15 Mar 2007, john kryst wrote:
> 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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