On 01/25/2011 04:32 AM, Maria Persico wrote: > I am exploring ModBase to build a model for the REcQ2 of arabidopsis > Thaliana(swiss prot acc: Q9FT73). > ModBase found 2 structures matching this target and after downloading > the coordinates file and also the showfile.chimerax file, I was able > to visualize with chimera both structures with apparently a > satisfactory relative orientation. Below I copy-paste the target > coverage: > > 2v1xA (63-592) crystal structure of human recq-like dna helicase > 1wudA (531-602) e. coli recq hrdc domain > > I wanted to know if there is an optimization step in the ModBase > pipeline to achieve this and if it is referenced somewhere...
ModBase just uses Modeller to build its models - it is not doing anything special. In fact, those two models are built entirely independently - they are not aligned or oriented. So the orientation you're seeing is entirely arbitrary - it depends on how the two template structures are oriented.
Ben Webb, Modeller Caretaker