Re: [modeller_usage] stuck even before begining - how to create the .ali file

Ariel Bensimon wrote: > I would like to use MODELLER to structurally align a protein domain with > a known PDB. But I am stuck. I could even create the basic .ali file. > Trying using the manual. Couldn't find the basic start of things

There is no requirement to make your initial alignment in Modeller - many people use different programs to do this. But if you did want to use Modeller, the basic tutorial at http://salilab.org/modeller/tutorial/basic.html takes you through a simple case.

Ben Webb, Modeller Caretaker