I am attempting to build a model from multiple templates, but I am
getting very bad results. After doing some tests I have discovered that
the problem lies most probably in the unwanted 3D orientation of the
blocks which the model is built from.
This is usually a symptom of incomplete optimization. You can improve
this in many cases by providing a better initial model (.ini file). Also
check to make sure the alignment templates have at least similar
structures - otherwise you're unlikely to get a sensible consensus
structure as a result. alignment.check() will usually warn about this.
To test this, I took a single PDB file and splitted it into three chunks
aligned as:
aaaaaaaaa-------------------------
------aaaaaaaaaaa-----------------
--------------aaaaaaaaaaaaaaaaaaaa
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
In this test, I would like to reconstruct the original structure. Is it
possible?
Very unlikely, since Modeller will build many of the distance restraints
that it would do if you used the complete PDB file as a single template.
For example, it cannot constrain the distance between the C and N
termini any more, because they are in different templates.
I tried to set the variable a.initial_malign3d=1, but the
modeller ends with the error "_modeller.ModellerError: fit2xyz_296E>
Number of equivalent positions < 3: 0"
This does a structural alignment between the three templates. This is
very unlikely to succeed, because you have such a small overlap between
them (hence the error about the number of equivalent positions being
insufficient).