On Saturday, 27 April 2019 06:35:11 Deepali Verma wrote:
> Dear all,
>
> While depositing the PDB to RCSB, the following query was raised about the
> TLS. Kindly advise to reporting the correct value of TLS origin
>
> *Query: *Please note that the reported TLS origin differs from the
> calculated one.
> May I change the reported origin to the calculated one ? (see below)
> Please advise.
I have no idea which is correct because I do not know how you obtained
the TLS model to begin with. Quite possibly neither is correct since
apparently the is some question about whether the TLS model parameters
correctly describe the model. Could it be that some symmetry operation
or other displacement was applied to the atoms without recalculating
the TLS?
In general the parameters making up a TLS model must be applied using
a specific origin. Most programs choose an origin for each TLS group
that is the center of mass for the atoms in that group.
But that is just a convenience.
It would be perfectly valid to choose the origin some other way.
If for some reason you need to change the origin you must recalculate
the TLS parameters to describe the original motion with respect to the
new origin rather than with respect to the previous origin.
I would suggest starting again with a clean slate.
Keep your atomic coordinates and re-refined the TLS model starting
from just the group description (no pre-calculated TLS parameters).
cheers,
Ethan
>
> TLS origin (calculated): -35.513 -14.735 9.557
> TLS origin (reported ): -36.928 2.341 -40.163
> LS origin differs from calculated(max_dev=49.72),group=1.
>
> TLS origin (calculated): -14.985 1.538 -0.012
> TLS origin (reported ): -53.962 -17.877 -32.831
> TLS origin differs from calculated(max_dev=38.98),group=2.
>
> TLS origin (calculated): -12.487 -26.271 -1.481
> TLS origin (reported ): -29.466 -24.119 -43.984
> TLS origin d! iffers from calculated(max_dev=42.50),group=3.
>
> TLS origin (calculated): -54.088 -18.130 -32.715
> TLS origin (reported ): -14.996 1.420 0.219
> TLS origin differs from calculated(max_dev=39.09),group=4.
>
> TLS origin (calculated): -29.406 -24.150 -43.971
> TLS origin (reported ): -12.570 -26.030 -1.269
> TLS origin differs from calculated(max_dev=42.70),group=5.
>
> TLS origin (calculated): -36.663 2.481 -40.041
> TLS origin (reported ): -35.412 -14.821 9.474
> TLS origin differs from calculated(max_dev=49.52),group=6.
>
>
--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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