This is the directory that goes with the Primer section in the MODELLER manual.

1) Finding structures related to the target sequence: SEARCH.TOP
 
2) Preparing initial family alignment of all structures and the target 
   sequence: MALIGN.TOP

3) Becoming familiar with the family fold and improving the alignment: 
   use RASMOL, QUANTA, or INSIGHT; no script files here.

4) Selecting the templates: CLUSTER.TOP

5) Modeling: GET-MODEL.TOP

6) Evaluating the models: use PROCHECK, QUANTA, INSIGHT, threading, etc; 
   no script files here.
