Re: [modeller_usage] Models from secondary structure and distance constraints alone?

Andrew D. Fant wrote: > This may seem like a rather strange question, but is it possible to get > Modeller to output a PDB structure based only on secondary structure > information and a few distance constraints (primarily dicystene > relationships).

Sure, you can do that. First, you can build a model using only the primary sequence: http://salilab.org/modeller/9v2/manual/node172.html

Next, you can build whatever restraints you want, optimize, and write out the PDB file: http://salilab.org/modeller/9v2/manual/node250.html

That example builds only stereochemical restraints, but you can add the same sorts of restraints that you can add to automodel, such as distance or secondary structure restraints.

Ben Webb, Modeller Caretaker