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!

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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.

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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

Hi John,

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

In phenix.refine you can reset B-factors (selected or all) before refinement: 1) you can ransomize them; 2) set to a value; 3) set to Wilson B. To do so, look modify_start_model scope: refinement.modify_start_model { adp { randomize = None set_b_iso_to = None set_biso_to_wilson_b = None convert_to_isotropic = False shift_b_iso_by = None } selection = None write_modified = None } Example: phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso_to=20 modify_start_model.selection="chain A and resid 10-20" This will set B=10 for the residues from 10 to 20 in chain A. Make sure to refine your model after such manipulation. Also, large B may indicate either lack of density or potential big movements so you may want to use TLS model.

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.

If you prepare this in CNS, you can manually replace the values. Also, make sure to put PHENIX (phenix.refine) as a program used. Let me know if you have any questions! Cheers, Pavel.