[it appears that I accidentally sent this to the listowner rather than the list. oops. sorry Ben]
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). I realize that without an alignment to a known structure, anything that is generated probably bears little resemblance to reality, but I have a relatively short fragment that isn't significantly related to anything in the PDB, and between the disulfide linkages and a couple other known constraints, there aren't that many ways that it could bend together. Basically, I'm trying to generate a consistent structure that is in a possible conformation that doesn't violate steric boundaries and such, without having to manually generate the coordinates from the helix and sheet parameters. Can anyone make any suggestions?
Thanks, Andy