On 3/22/10 2:50 AM, abdullah ahmed wrote: > I have a few very long (and perhaps naive) questions regarding "Table > 6.1: List of physical Restraints types"

For reference, this is the table at http://salilab.org/modeller/9v7/manual/node245.html#21703

> 1. If the Hydrogen bonding restraint is applied, does it > automatically incorporate all possible Hydrogen bonds in the file, > or do the specific hydrogen bonding atoms have to be specified? > (Also could you maybe provide a short piece of code showing how > this restraint can be applied?)

This table is not a list of restraints. It is a list of categories into which you can place your restraints. Thus, the names are essentially meaningless - they are just a convenience for the purpose of weighting different groups of restraints.

physical.h_bond is used as the category for restraints between two beta-strands generated by secondary_structure.sheet(); see http://salilab.org/modeller/9v7/manual/node213.html for an example.

> 2. Are the Phi, Psi, omega, and Chi restraints used to lock the > angles of the backbone and the the side chain into specific values > or are they used for something else all together?

These are used by Restraints.make() - see http://salilab.org/modeller/9v7/manual/node196.html - when building the various homology-derived dihedral restraints. See that URL for more information.

> 3. What do the accessibility, absposition, dihedral_diff and SAX > restraints do?

They are used as the categories for some types of restraints. accessibility, absposition and dihedral_diff are typically used as the category for the similarly-named features at http://salilab.org/modeller/9v7/manual/node97.html. The SAXS category is for SAXS restraints, which are experimental and incomplete, and thus not currently used.

Ben Webb, Modeller Caretaker