Phenix TLS refined model feeding into next round of refinement
Hi, I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement? Thank you. Daqi Tu
Hi,
I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement?
- it seems to me extremely weird if you do one refinement run with TLS and then the next one without TLS. I can't see a reason for this. - by removing ANISOU records you completely invalidate the results of previous TLS refinement; - phenix.refine tries to decide automatically where the input ANISOU come from. If input file contains ANSIOU and resolution is low enough and TLS refinement is not requested then phenix.refine simply removes ANISOU and continues. Obviously, this means the previous results of TLS refinement are all completely invalidated. More details: 1) http://www.phenix-online.org/newsletter/ articles "TLS for dummies" and "On atomic displacement parameters (ADP) and their parameterization in PHENIX". 2) http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p... 3) http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf Pavel.
Pavel, Thanks. This answered my concern. I wanted to use TLS, just not anisotropic INDIVIDUAL B factor refinement, which at my resolution is not high enough. I was just worried the ANISOU record will fool the program into anisotropic individual B factor refinement. But clearly when TLS is still requested, Phenix knows what to do. cheers, Daqi On 7/20/2011 5:39 PM, Pavel Afonine wrote:
Hi,
I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement?
- it seems to me extremely weird if you do one refinement run with TLS and then the next one without TLS. I can't see a reason for this.
- by removing ANISOU records you completely invalidate the results of previous TLS refinement;
- phenix.refine tries to decide automatically where the input ANISOU come from. If input file contains ANSIOU and resolution is low enough and TLS refinement is not requested then phenix.refine simply removes ANISOU and continues. Obviously, this means the previous results of TLS refinement are all completely invalidated.
More details:
1) http://www.phenix-online.org/newsletter/ articles "TLS for dummies" and "On atomic displacement parameters (ADP) and their parameterization in PHENIX".
2) http://www.phenix-online.org/presentations/latest/pavel_refinement_general.p...
3) http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf
Pavel.
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participants (2)
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Daqi Tu -
Pavel Afonine