Refinement with rigid-base TLS parameterization has been previously
explored:
Holbrook, Dickerson, Kim (1985) Acta Cryst B41, 255-262.
(the photocopy is located in the pile of dust that I maintain adjacent
to my desk)
Ethan Merritt wrote:
> On Thursday 15 July 2010, Huw Jenkins wrote:
>
>> Hi,
>>
>> I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base.
>>
>
> Aside from issues of describing the groups at all, I would not recommend
> this as a refinement protocol. The number of atoms in each group is too
> small for TLS refinement to be well-behaved in the absence of additional
> restraints that the current generation of programs (refmac, phenix.refine)
> does not implement.
>
> It is in principle an attractive idea to treat at least the planar bases
> as individual TLS groups, but I have not had the time or opportunity to
> explore this in practice. Ideally, one might like to try constraining the
> group so that the glycosyl bond defined the libration axis (see for
> instance the section on ADP representations in the Newsletter that Pavel
> Afonine posted recently). Unfortunately again this is not implemented in
> current refinement programs.
>
> My gut feeling is that the best TLS description would be each base
> (or base pair) in its own group, the use TLSMD to analyse and assign groups
> for the backbone atoms. But again I have no actual experience with this,
> so it's only a suggestion.
>
> Ethan
>
> Just as an aside:
> The B factors in the PDB file 1j75, which I think corresponds to the paper
> you cite, are very far from reasonable. I would not use this structure as
> an example of success in choosing a refinement protocol for ADPs. Although
> I also note that it is possible the B factors archived in the PDB file have
> become mangled during deposition of the output from a non-standard protocol.
>
>
>
>> When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined:
>>
>>
>> TLS origin for group 1 -3.1622999 -6.9280601 -9.6330261
>> TLS origin for group 2 0.0000000 0.0000000 0.0000000
>> TLS origin for group 3 0.0000000 0.0000000 0.0000000
>>
>> TLS group 1:
>> T tensor ( 1) = 0.046 0.115 0.103 -0.003 -0.008 0.087
>> L tensor ( 1) = 1.341 1.887 5.684 0.509 -2.040 -0.436
>> S tensor ( 1) = 0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060
>>
>> TLS group 2:
>> T tensor ( 2) = 0.031 0.031 0.031 0.000 0.000 0.000
>> L tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000
>> S tensor ( 2) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>>
>> TLS group 3:
>> T tensor ( 3) = 0.031 0.031 0.031 0.000 0.000 0.000
>> L tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000
>> S tensor ( 3) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>>
>>
>> An excerpt from my tlsin is below:
>>
>> TLS
>> RANGE 'B 3.' 'B 3.' P
>> RANGE 'B 3.' 'B 3.' O1P
>> RANGE 'B 3.' 'B 3.' O2P
>>
>> TLS
>> RANGE 'B 3.' 'B 3.' C1*
>> RANGE 'B 3.' 'B 3.' C2*
>> RANGE 'B 3.' 'B 3.' C3*
>> RANGE 'B 3.' 'B 3.' C4*
>> RANGE 'B 3.' 'B 3.' C5*
>> RANGE 'B 3.' 'B 3.' O2*
>> RANGE 'B 3.' 'B 3.' O3*
>> RANGE 'B 3.' 'B 3.' O4*
>>
>>
>> TLS
>> RANGE 'B 3.' 'B 3.' N1
>> RANGE 'B 3.' 'B 3.' C2
>> RANGE 'B 3.' 'B 3.' O2
>> RANGE 'B 3.' 'B 3.' N3
>> RANGE 'B 3.' 'B 3.' C4
>> RANGE 'B 3.' 'B 3.' O4
>> RANGE 'B 3.' 'B 3.' C5
>> RANGE 'B 3.' 'B 3.' C6
>>
>> I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated!
>>
>> Thanks,
>>
>>
>> Huw
>>
>>
>>
>> --
>> Dr Huw Jenkins
>> Astbury Centre for Structural Molecular Biology
>> University of Leeds
>>
>>
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