On Tuesday 06 February 2007 13:48, JEREMIAH R WAGNER wrote:
> Hello All,
> Our group is having discussion about B values after TLS and isotropic
> refinement in Refmac. Our basic question is:
> Does the B value for the individual atoms in the pdb consist of both
> the B values from TLS and isotropic refinement parameters,
> or just for isotropic refinement.
The B values in individual ATOM records are the amount by which the
total B for that atom differs from the TLS model. In priciple they
can be either positive or negative, but since many programs freak out
when they encounter negative "B values" we bias the TLS model so that
the residual should always be positive. Sometimes we under-estimate,
and the bias is not sufficient. This is one way that TLS+Biso
refinement can go bad, because the residual B's bottom out at 2.
To reconstruct the isotropic equivalent B corresponding to the
sum of contributions from TLS and Biso, you can use the script
given below. Note that doing this loses the anisotropic component
of the TLS model, so you will degrade your model.
#/bin/csh
if ( {$#} < 1 || $1 == "-h" ) then
echo ""
echo " Usage:"
echo " tls_correct 1XYZ"
echo ""
echo " where 1XYZ is the 4 letter PDB identifier code for a structure"
echo " containing an explicit TLS model description in the header records."
echo " This script will create an output file 1XYZ_bcor.pdb"
echo " in which the TLS description has been applied to all relevant"
echo " atoms, creating a file with ANISOU descriptions of these atoms"
echo " rather than TLS + Biso."
echo ""
exit
endif
#
tlsextract XYZIN {$1}.pdb TLSOUT {$1}.tlsout
tlsanl XYZIN {$1}.pdb TLSIN {$1}.tlsout XYZOUT {$1}_bcor.pdb << EOF
BRESID true
ISOOUT full
END
EOF
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