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Re: [modeller_usage] Restraints in table 6.1

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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
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