Michael Mayhew wrote: ... > I also referred to the user manual and found that in my version of > modeller, malign_3d has been deprecated and that I should use salign. > However, salign (in the context of the tutorial exercise) does not > return an object that can be used to continue the tutorial.
The tutorial has not yet been updated to use salign. malign3d still works just fine - we just recommend using salign for serious alignments.
... > pdbnam_____E> Filename for PDB code not found: 1b8p
Obviously to do a structural alignment, you need the structures. So Modeller tries to read in PDB files for each one, and it's reporting that it can't fin the 1b8p PDB. You can either get these PDB files from PDB itself, or you can download the basic tutorial input files from the link at the top of the basic tutorial page, which includes all of the needed input PDBs.
Ben Webb, Modeller Caretaker