Dear modellers:
I had got some questions when I tried to build a model on a basis of 3
different structures. I used full_homol.top (or model.top) script of the
Modeller4. The sequence identities were 59, 54, and 47%. The resolution of
structures was 1.8 - 2 A. The alignment was perfect. Nevertheless, at the
end of an optimization procedure, the objective function was ca.3000 -
4000. When I have used only one structure (with the sequence identity
59%), the same optimization procedure resulted in models with the
objective function of 600 - 700.
Probably, for this particular case only one structure was necessary. However,
it is still unclear to me, why using different structures increased the
objective function value by an order?
Which role does the CLUSTER_CUT option play for the TRANSFER_XYZ command?
Changing it to 1.0 (as recommended by Manual) didn't let the Modeller4
run. An error message was reported:
trfxyz_E> structures not isomorphic: i,na,na",nr,nr" 2 1147 1129 150 144
What does it mean?
Thanks in advance,
Gulshat
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Gulshat Ibragimova, Ph.D.
EMBL, Postfach 102209
69012 Heidelberg, FRG
Tel: +49 (0)6221 387466, Fax: +49 (0)6221 387517