July 2012 - phenixbb - phenix-online.org

Question about mr-sad
by Edward A. Berry 02 Jul '12

02 Jul '12

in doing SAD phasing with the option: input_partpdb_file=MR.pdb Is it assumed MR.pdb is already located in the cell, or is it a model to be used in MR assisted by information from the heavy atom sites? Thanks, eab

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Re: [phenixbb] Default anisotropic B-factor refinement in phenix.refine?
by Filip YABUKARSKI 02 Jul '12

02 Jul '12

Hello again, First thank you very much for the response But in this case after the second run of phenix.refine i will lose the TLS contribution and the anisoU lines (?). How am I supposed to continue with TLS then (given it lowers my R factors i would be happy to keep it) and be sure that i do not refine anisotropic ADPs? Or you mean that i can do the 2 consecutive runs (with and without TLS) in the end of the refinement? Sorry if I got something wrong Filip On 2012-07-02 18:58, Pavel Afonine wrote: > Hi Filip, > > phenix.refine manual may need an update.. > > At 3A resolution if you run two consecutive refinements first with > TLS and the next one without TLS then in the second run anisotropic > ADPs will be converted to isotropic automatically. This is done by > phenix.refine to prevent accidental refinement of individual > anisotropic ADPs in such cases. The keyword and threshold are: > switch_to_isotropic_high_res_limit=1.5. > > Pavel > > On 7/2/12 9:47 AM, Filip YABUKARSKI wrote: >> Hello, >> >> I recently started to refine a structure with phenix.refine for a >> first time. It is a 3A dataset with NCS of 8. For the refinement i >> wanted to use TLS groups as well as individual B-factors >> (data/parameter ratio should be fine with ncs of 8) and after several >> cycles of refinement i get the Rfac of 20 and Rfree of 24 which is >> quite good (i also use simulated annealing, Secondary structure >> restraints and NCS restraints). Re-reading the refinement manual I >> realized that by using a PDB file which comes from a phenix.refine >> with TLS in the next refinement i am probably doing an anisotropic >> B-factor refinement for each atom, which in my case is not justified. >> I found a post on ccp4bb from 19 Fev 2009 discussing this issue but >> for me it is still not very clear. By reading the PDB i got from >> phenix.refine (version 1.7.3) it is not very clear (at least for me) >> if the refinement was with TLS groups and individual isotropic >> B-factors or with anisotropic B-factors. Basically my question is: if >> the input PDB has already anisoU records from a previous phenix.refine >> with TLS groups is the new phenix.refine going to use isotropic >> individual B-factors or anisotropic ones? (Even if in my case one can >> assume that i can probably use anisotropic B-factor refinement (24000 >> unique reflections with ncs of 8 vs. 6000 atoms in total) this is >> rarely the case for non-atomic resolution datasets) I would be very >> happy if someone gives an explanation. Many thanks >> >> Cheers >> Filip

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Default anisotropic B-factor refinement in phenix.refine?
by Filip YABUKARSKI 02 Jul '12

02 Jul '12

Hello, I recently started to refine a structure with phenix.refine for a first time. It is a 3A dataset with NCS of 8. For the refinement i wanted to use TLS groups as well as individual B-factors (data/parameter ratio should be fine with ncs of 8) and after several cycles of refinement i get the Rfac of 20 and Rfree of 24 which is quite good (i also use simulated annealing, Secondary structure restraints and NCS restraints). Re-reading the refinement manual I realized that by using a PDB file which comes from a phenix.refine with TLS in the next refinement i am probably doing an anisotropic B-factor refinement for each atom, which in my case is not justified. I found a post on ccp4bb from 19 Fev 2009 discussing this issue but for me it is still not very clear. By reading the PDB i got from phenix.refine (version 1.7.3) it is not very clear (at least for me) if the refinement was with TLS groups and individual isotropic B-factors or with anisotropic B-factors. Basically my question is: if the input PDB has already anisoU records from a previous phenix.refine with TLS groups is the new phenix.refine going to use isotropic individual B-factors or anisotropic ones? (Even if in my case one can assume that i can probably use anisotropic B-factor refinement (24000 unique reflections with ncs of 8 vs. 6000 atoms in total) this is rarely the case for non-atomic resolution datasets) I would be very happy if someone gives an explanation. Many thanks Cheers Filip

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