Editing ResDe (section)

===Restraint Definer===

[[File:RestraintDefinerView.png ‎|right|frameless|500px]]Restraint Definer is a PyMol plugin. After installation the user can access this tool by simply using the plugin menu in PyMol. The user will first open their structure in PyMol. Restraint Definer has three modes; 'Single Restraint', 'Helix (click)', 'Helix (range)'.
TO CHANGE RESTRAINT DEFINITION MODE: ResDe's Restraint Definer menu is in the right hand column of PyMol. The top button in this menu is the 'Mode' button; by default it reads 'Define Single Restraints'. clicking on this button will cause a drop menu to appear from which the user can select either 'Define Single Restraint', 'Define Helix (click)', 'Define Helix (range)' mode.

Upon running Restraint Definer (via the Plugin menu), the program will be in 'Single Restraint' mode by default. To define a restraint in this mode, the user simply clicks on the two atoms they wish to restrain. This will cause a dotted line to form between the two atoms (this is simply a variation of PyMol's measurement tool). When in 'Helix (click)' mode, the user clicks on the two helix termini residues (any atom), order does not matter. Restraints (dotted lines) will appear between the carbonyl oxygens and the n+4 backbone nitrogens along the entire helix. When in 'Helix (range)' mode, a widow comes up asking the user which object to perform the operation on(i.e. if you are working on ABCD.pdb you would choose object ABCD). After selecting the object another widow asks the user about the helix to be defined including chain ID and residue number range. Also, the user can sleek to use a threshold length and enter that length. If a potential restraint in the residue range is longer than the set threshold the restraint will not be created.

Under the 'Undo" menu the user can undo previous actions; remove last restraint and remove last helix. 'Customize Bond Parameters' allows the user to edit the ideal bond length, slack, and sigma from their default values 2.9, 0 , 0.02, respectively. 'Restrain All Helices' brings up a window where the user can dictate how the operation to define all helices is handled. This includes the threshold setting as explained above (see 'Helix (range) mode). Also, the user can select to run DSS, PyMOL's internal secondary structure assignment algorithm.

As restraints are added, a new collapsable object menu will appear in PyMol called 'Restraints'. This menu contains all restraints that have been defined by the user. Inevitably wrong atoms will be clicked leading to inappropriate restraints. These can be removed by deleting the restraint object (the dotted line) under the Restraints menu (the objects are named using the residue numbers and atom names of the two atoms that are restrained).

After defining restraints the user can save the restraints by clicking on the 'Save Restraint Definitions' button. ResDe will ask the user which restraint format that they wish to save their file in, Phenix or ccp4. This restraint definition file is ready to be used in structure refinement using the respective refinement software. If you don't complete defining restraints in one session you can save the restraint definitions and bring them up later (using Restraint Checker) to add more restraints.