TLS refinement in phenix
Dear all, I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this Regards Mirage singh Protein crystallography Laboratory IMTECH (IMTECH is a research establishment of CSIR, india) Chandigarh
They are "pseudo-ANISOU" records that contain the TLS contribution. Nothing to worry about, they are not "real" ANISOU records as in the case of anisotropic temperature factor refinement. Fred. Mirage Singh Baliyan wrote:
Dear all, I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this
Regards Mirage singh
Protein crystallography Laboratory IMTECH (IMTECH is a research establishment of CSIR, india) Chandigarh http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signa...
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They are "pseudo-ANISOU" records that contain the TLS contribution. Nothing to worry about, they are not "real" ANISOU records as in the case of anisotropic temperature factor refinement.
Now I don't understand this -:) What are the "pseudo-ANISOU", "real" ANISOU ? I think it's just good to realize which model parameterization is used and what it means, then there will be no surprise-results. TLS is a constrained anisotropic refinement. Following your "pseudo" vs "real" analogy, we can then call coordinates in ATOM records obtained after NCS constrained refinement as "pseudo-ATOM", and those obtained after regular restrained refinement as "real" ones. Pavel.
What I meant is that they do not correspond to full anisotropic refinement (6 parameters for an ellipsoid) for each atom. Nothing more was meant. Pavel Afonine wrote:
They are "pseudo-ANISOU" records that contain the TLS contribution. Nothing to worry about, they are not "real" ANISOU records as in the case of anisotropic temperature factor refinement.
Now I don't understand this -:) What are the "pseudo-ANISOU", "real" ANISOU ? I think it's just good to realize which model parameterization is used and what it means, then there will be no surprise-results. TLS is a constrained anisotropic refinement.
Following your "pseudo" vs "real" analogy, we can then call coordinates in ATOM records obtained after NCS constrained refinement as "pseudo-ATOM", and those obtained after regular restrained refinement as "real" ones.
Pavel.
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Praji, This has been discussed a number of times in CCP4BB. TLS is nothing but a cheaper (parameter wise) way to incorporate anisotropic aspects in the refinement when the resolution is not as high as, lets say 1.5A. Therefore, it is only just if the ANAISOU record is also there. Now, it depends on the individual developers how they want to write the output. Refmac does it in the header of the pdb, Phenix does it right after the ATOM record. In general, try to stick to one program. HTH, Partha On Fri, Jul 2, 2010 at 4:08 PM, Mirage Singh Baliyan < [email protected]> wrote:
Dear all, I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this
Regards Mirage singh
Protein crystallography Laboratory IMTECH (IMTECH is a research establishment of CSIR, india) Chandigarh
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TLS is nothing but a cheaper (parameter wise) way to incorporate anisotropic aspects in the refinement when the resolution is not as high as, lets say 1.5A.
This is one way of looking at this. The other one, that I prefer, is to look at this as a way of modeling different kinds of atomic/molecular motions, and therefore to have a more sensible physical model for them (#30): http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_p... So, ideally, one would use TLS at any resolution.
Now, it depends on the individual developers how they want to write the output. Refmac does it in the header of the pdb, Phenix does it right after the ATOM record.
I was thinking that the latest versions of Refmac output total ADP too (or at least there is an option for this)... Can someone clarify this? Pavel.
Hi Mirage,
I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this
see slides 30-36 here: http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_p... which explain this. Briefly: "TLS refinement" = "Constrained anisotropic refinement", therefore ANISOU records. Pavel.
Hi Mirage,
I am refining a 2.25 A structure in phenix using TLS parameters. In the generated PDB there is one ANISOU record along with the ATOM record. I am not understanding this. can anybody help me about this
this is explained in details in the latest PHENIX Newsletter that came out a few days ago: http://www.phenix-online.org/newsletter/ Pavel.
participants (4)
-
Mirage Singh Baliyan -
Partha Chakrabarti -
Pavel Afonine -
Vellieux Frederic