Hi, When TLS is used, phenix.refine gives 6 ANISOU B factors for each atoms. But we also get a number at the normal isotropic B factor position. If that number is the isotropic B factor, how was it calculated? Did you use something like the following? Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3 Is it the same as the output from tslanl if using refmac5? -- Jianghai
Hi Jianghai, here is the copy from phenix.refine manual (http://phenix-online.org/documentation/refinement.htm): " When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual)." If ANISOU records are present then the equivalent isotropic B-factors in ATOM records are always derived from ANISOU as described above (in accordance with PDB format). I do not know if it is the same as TLSANL. Pavel. On 5/10/2008 7:09 AM, Jianghai Zhu wrote:
Hi,
When TLS is used, phenix.refine gives 6 ANISOU B factors for each atoms. But we also get a number at the normal isotropic B factor position. If that number is the isotropic B factor, how was it calculated? Did you use something like the following?
Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3
Is it the same as the output from tslanl if using refmac5?
-- Jianghai
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Hi, Pavel, Thanks for the answer. If I compare the isotropic equivalent B-factor after TLS refinement to the isotropic B-factor without TLS refinement, will they have the same trend? I want to use the B-factor distribution to describe the ordered and disordered region in the structure, will the TLS refinement skew that? Thanks. -- Jianghai On May 10, 2008, at 10:47 AM, Pavel Afonine wrote:
Hi Jianghai,
here is the copy from phenix.refine manual (http://phenix-online.org/documentation/refinement.htm):
" When refining TLS, the output PDB file always has the ANISOU records for the atoms involved in TLS groups. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual)."
If ANISOU records are present then the equivalent isotropic B- factors in ATOM records are always derived from ANISOU as described above (in accordance with PDB format).
I do not know if it is the same as TLSANL.
Pavel.
On 5/10/2008 7:09 AM, Jianghai Zhu wrote:
Hi,
When TLS is used, phenix.refine gives 6 ANISOU B factors for each atoms. But we also get a number at the normal isotropic B factor position. If that number is the isotropic B factor, how was it calculated? Did you use something like the following?
Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3
Is it the same as the output from tslanl if using refmac5?
-- Jianghai
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Hi Jianghai,
If I compare the isotropic equivalent B-factor after TLS refinement to the isotropic B-factor without TLS refinement, will they have the same trend?
yes, only if: 1) the choice of TLS groups is correct; 2) the restraints on isotropic individual B-factors are not too tight.
I want to use the B-factor distribution to describe the ordered and disordered region in the structure, will the TLS refinement skew that?
I'm not sure what exactly you want to do here. But anyway, by using TLS model you better describe atomic ADP: TLS models global domain motion and individual B-factors model local atomic vibrations; that is each kind of motion receives dedicated parameterization (which is good). However, if you model everything with individual B-factors (no TLS) the similarity restraints are always used and they tend to remove TLS contribution making final B-factors less adequate. Pavel.
Pavel, Thanks. I actually just want to do a very simple thing. In the days before TLS refinement, we use B-factor distributions to find the ordered and less ordered regions in the structure, i.e. low B- factors, ordered region and high B-factors, less ordered region. I just wondered if I can still do that with the isotropic equivalent B- factors after a TLS refinement. Or should I just get a real isotropic B-factors distribution by re-refining the model without TLS? -- Jianghai On May 11, 2008, at 2:03 AM, Pavel Afonine wrote:
Hi Jianghai,
If I compare the isotropic equivalent B-factor after TLS refinement to the isotropic B-factor without TLS refinement, will they have the same trend?
yes, only if: 1) the choice of TLS groups is correct; 2) the restraints on isotropic individual B-factors are not too tight.
I want to use the B-factor distribution to describe the ordered and disordered region in the structure, will the TLS refinement skew that?
I'm not sure what exactly you want to do here. But anyway, by using TLS model you better describe atomic ADP: TLS models global domain motion and individual B-factors model local atomic vibrations; that is each kind of motion receives dedicated parameterization (which is good). However, if you model everything with individual B-factors (no TLS) the similarity restraints are always used and they tend to remove TLS contribution making final B-factors less adequate.
Pavel.
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Hi Jianghai, I see now. The problem is that if you do individual B-factors refinement (no TLS) then the result will be affected by restraints. Ideally you would need to do this without restraints, but this is not practical. To obtain the estimate you want I would simply do group B-factors refinement with one B per residue. In this case the restrains are not used. It would be good to compare the results with TLS and individual only refinement. Do it in two steps: re-set all B to Wilson B (or to current average), then do group B refinement: 1) phenix.pdbtools model.pdb set_b_iso=25 2) phenix.refine model_b25.pdb data.mtz strategy=group_adp Note, the default is one B per residue. You can specify your own selections. Pavel. On 5/11/2008 7:00 AM, Jianghai Zhu wrote:
Pavel,
Thanks. I actually just want to do a very simple thing. In the days before TLS refinement, we use B-factor distributions to find the ordered and less ordered regions in the structure, i.e. low B- factors, ordered region and high B-factors, less ordered region. I just wondered if I can still do that with the isotropic equivalent B- factors after a TLS refinement. Or should I just get a real isotropic B-factors distribution by re-refining the model without TLS?
-- Jianghai
On May 11, 2008, at 2:03 AM, Pavel Afonine wrote:
Hi Jianghai,
If I compare the isotropic equivalent B-factor after TLS refinement to the isotropic B-factor without TLS refinement, will they have the same trend?
yes, only if: 1) the choice of TLS groups is correct; 2) the restraints on isotropic individual B-factors are not too tight.
I want to use the B-factor distribution to describe the ordered and disordered region in the structure, will the TLS refinement skew that?
I'm not sure what exactly you want to do here. But anyway, by using TLS model you better describe atomic ADP: TLS models global domain motion and individual B-factors model local atomic vibrations; that is each kind of motion receives dedicated parameterization (which is good). However, if you model everything with individual B-factors (no TLS) the similarity restraints are always used and they tend to remove TLS contribution making final B-factors less adequate.
Pavel.
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Pavel Afonine