Hi,

It is OK that the obj func changed as much as it did. When one has several templates, the obj func contains more restraints, they are more frustrated, and more difficult to satisfy at the same time because they are not entirely consistent with each other. So the obj func value gets worse. Just make sure that PROCHECK does not complain about the model; this is likely since the alignment is good and your templates are probably similar structurally. In general it is better to use a couple of templates that are roughly equally similar to the target than just one template. This gives MODELLER a chance to pick (automatically) the best template for each "region" along the sequence (see discussion of that in our Proteins Suppl I, 1997 paper).

Please do not use change cluster_cut. It is not documented ... Maybe in the next version it will be. But if you really want to see what goes on, please check $MODINSTALL/bin/__cluster.top. The error message that you got is ok, you should get it, because the templates and the target do not have exactly the same number, kind and order of atoms.

Best, Andrej

> > 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 > > --------------------------------------------------------------------- > Gulshat Ibragimova, Ph.D. > EMBL, Postfach 102209 > 69012 Heidelberg, FRG > Tel: +49 (0)6221 387466, Fax: +49 (0)6221 387517 >