Re: [phenixbb] Few questions

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

regards john

On 3/15/07, Pavel Afonine 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. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb