On 6/10/10 12:30 PM, David RodrÃguez wrote: > I am interested in making a 3D structural alignment of the resulting > models with their template(s). I have included the "a.final_malign3d = > True" line in the script as stated in the manual, and the *_fit.pdb > files were generated. However, none of the models are correctly aligned > to the template.
That's intriguing, although I can't say for sure why it's happening without seeing your input files. My guess is that either a) you have very low sequence identity, so there is not enough conserved structure for malign3d to be able to make the correct alignment, or b) you have multiple templates which do not overlap well, and it's having a hard job aligning all of the models with all of the templates.
Ben Webb, Modeller Caretaker