Hi all

Can anyone help with an example of the use of additional restraints involving pseudoatoms? I've read the relevant sections of the manual

http://salilab.org/modeller/manual/node99.html http://salilab.org/modeller/FAQ.html#8

and it's still not clear to me. The FAQ has this example of a user-added restraint

SET ATOM_IDS 'CA:35:A' 'CA:40:A' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 0.1

How to define pseudo-atoms instead of single real atoms?

Alternatively, if the restaint were added in a file, how to specify defined pseudo-atoms within the format?

R Form Modality Feature Group Numb_atoms Numb_parameters 0 Atom_indices Parameters R 3 1 1 1 2 2 0 437 28 1.5000 0.1000

In my case, I'd like to make a helix (which I'll define as a pesudoatom) in a large insertion pack better, more compactly against the rest of the protein. Has anyone any experience with similar situations?

Many thanks in advance

Daniel Rigden