Dear Ben,
thanks for your prompt reply!
Modeller Caretaker wrote: > Raik Gruenberg wrote: >> So to what extend differs the multiple-template treatment of Modeller >> 9 from previous versions? Do I need to use different parameters for >> multi-template modeling in the new version? Or is the general default >> modeling protocol different now? > > The multiple-template treatment did not change at all between Modeller 8 > and Modeller 9, so I'm surprised that you're seeing such different models. > > I can't deduce anything more from your output PDB files. If you can make > a zip file of your inputs (see > http://salilab.org/modeller/manual/node10.html) then I can take a look > to see whether you're running into a bug.
I double-checked things this morning and I am indeed getting very different results from the two modeller versions running on the same machine, using the same alignment, structures etc. I am going to send you the complete input and the different results in a separate e-mail.
The large number of templates isn't perhaps the main issue. I just repeated the test with only the three best templates (42 - 86% ID). And again modeller 8 fares well but modeller 9 produces knots and wrong topologies in many of the 10 output models. Of course this is still using the same automatic input alignment which may be less than perfect (T-Coffee consensus of a structure alignment of *all* 10 templates combined with 2 more alignments from a global sequence search).
> > One obvious thing to check is the generated .rsr file for both 8 and 9. > If you're getting different models, then either the multiple-template > treatment (or some other part of the restraints generation) is making a > different set of restraints, or you have the same restraints in both > cases but they are being optimized differently.
The first page or so of this file is identical between the two versions but then things seem to diverge. Please have a look yourself.
> >> So here is our (old-style) input file: >> > > Is this being generated by the Biskit framework? If so, why does it > generate deprecated TOP files when Python scripts give you more > flexibility?
:-) Well, we implemented the homology modeling module of Biskit already back in 2004 starting with Modeller 6 (!) if I remember right. We just never really advertised it. I would say, it testifies to your good software development that the same wrapper is still working 3 versions later. But you have a point there. We should switch the default template to the current standard also to allow better customization. Besides, and this really leads off-topic now, we also are not actually mixing "your python" with "our python". Seeing how you are transforming Modeller into a full-fledged python library, that would probably give interesting possibilities, though perhaps at the cost of simplicity, modularity, "installability", ... Anyway, that would make a different discussion.
Thanks a lot for your help! Greetings, Raik
> > Ben Webb, Modeller Caretaker