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The Volume pulldown contains commands that allow you to calculate molecular volumes, perform Boolean operations on molecules and volumes, create graphical representations of molecular volumes, and modify the appearance of the graphical representations.
Volume Pulldown
Create
The Volume/Create command is used to calculate volumes for molecules, assemblies of molecules, and sets of conformations in trajectories. It also has the ability to create several types of graphical representations of the volumes.
Boolean
The Volume/Boolean command is used to perform Boolean volumetric operations involving both molecules and volumes.
Grid_Setup
The Volume/Grid_Setup command is used to specify the size, location, and resolution of the volume's grid.
Align
The Volume/Align command is used to align a volume to the coordinate system of a reference molecule.
Color
The Volume/Color command is used to change the color of a volume's point cloud, contour, or label.
Label
The Volume/Label command is used to add, move, and remove volume labels. The text of the label is the volume name.
Display
The Volume/Display command is used to independently specify which components of the volume to display--the label, contour, and point cloud. A contour can be displayed as a line contour or a solid contour.
List
The Volume/List command is used to report the volume (in cubic angstroms) occupied by an existing volume and the resolution of the volume's grid.
The Overlap pulldown contains commands allowing you to superimpose a group of molecules using either rms alignment or molecular field similarity optimization. You can perform either rigid or flexible fitting. In the latter case, you can select bonds in the molecules that are rotated in the optimization process.
Overlap Pulldown
After the optimization process, the molecules are aligned on the screen automatically. You can form an assembly object in order to move and rotate all molecules together. You can also display each molecule with a distinctive color. In addition, you may create a table detailing rms or similarity values for each pair of molecules.
Define
The Overlap/Define command is used to define atoms to be superimposed and rotatable bonds to be optimized during the superimposition process. This command is also used to execute the rms overlap calculation. You use this command to add, delete, and list atom pairs and rotatable bonds.
Field_Fit
The Overlap/Field_Fit command is used to compare molecular fields--combinations of electrostatic potentials and steric shape--among two or more molecules, and/or to superimpose these molecules by optimizing the similarity as a function of position. In the fitting process, bonds among the molecules can be rotated to find the conformations that have the highest similarity.
Display
The Overlap/Display command specifies whether or not to display selected atom pairs or rotatable bonds with special highlights and whether to show labels of selected atoms.
The SC_Search pulldown contains commands that allow you to set up a systematic conformational search, run it, and load the results into Insight II. A systematic conformational search is set up by specifying the parameters for the search with the commands Set_Ring_Closure, Set_Rot_Bond, Set_Distance, Set_Dist_Map, Scale_Radii, and Set_Energy_Params. The commands in the Background_Job pulldown are used to prepare for running the systematic conformational search as a background job. The search calculation is initiated with the SCS_Run command. The results of a search are loaded into the Insight II program with the Load command.
SC_Search Pulldown
Set_Ring_Closure
The SC_Search/Set_Ring_Closure command is used to create and edit a list of ring closure bonds and the corresponding ring closure constraints. This command is used for systematic searching on cyclic systems. You must first define the closure bonds that are broken during search calculations, then you can proceed with definition of rotatable bonds through the SC_Search/Set_Rot_Bond command.
Set_Rot_Bond
The SC_Search/Set_Rot_Bond command is used to create and edit a list of rotatable bonds for the systematic conformational search. These bonds constitute the torsion angles about which the systematic conformational search is performed.
Set_Distance
The SC_Search/Set_Distance command is used to create a list of atom-atom distance constraints that constitute a set of acceptance criteria for conformations generated in a search. It allows you to create a new specification, read a list of specifications from a previous systematic search parameter file, or extract distance constraints from the output file of a previous search.
Set_Dist_Map
The SC_Search/Set_Dist_Map command is used to set up a new distance map or a distance map that maps the results of a prior search.
Scale_Radii
The SC_Search/Scale_Radii command is used to apply scaling factors to the van der Waals radii of all atoms, of hydrogen bond donor/acceptor pairs, or of vicinal (1-4) atoms.
Set_Energy_Params
The SC_Search/Set_Energy_Params command specifies how energy calculation and screening will be performed when the SCS_Run command is invoked. This command specifies the maximum number of conformers to keep, the energy threshold for screening out unstable conformers, whether or not to perform energy minimization for each conformer, and several parameters used by the energy calculation routines.
Set_Filter_Params
The SC_Search/Set_Filter_Params command is used to control and customize the duplicate removal process applied to the conformations produced by a systematic search. For example, if local symmetry in the search molecule is to be considered, you specify the RMS and energy tolerances and the set of atoms considered when comparing conformations. You can also specify which atoms are used for the RMS duplicate matching by specifying one of a list of atom types, e.g., Heavy Atoms (all atoms other than hydrogens) or a specific list of atoms that you create and edit yourself.
SCS_Run
The SC_Search/SCS_Run command is used to initiate a systematic conformational search; to estimate the number of conformations that will be found, prior to actually running the search; or to perform post-processing on the results of a previous search (such as energy filtering or distance map calculation).
The progress of a search can be monitored by using the Background_Job/Completion_Status command. You can interrupt a searching job and keep the partial results by executing the Background_Job/Kill_Bkgd_Job command with the Save_Output parameter toggled on.
Load
The SC_Search/Load command is used to load the results of a systematic conformational search into the Insight II program. The results are loaded in the form of a trajectory. Trajectories can be loaded from both XDR_TOR and ARC files and it is possible to load only part of a trajectory. The commands in the Vector_Map, Distance_Map, and Conformer pulldowns, and the commands in the Analysis or DeCipher modules can then be used to analyze the results.
You can monitor the angles of defined torsions and distances between constrained atoms by toggling the Dihedral_Monitor and Distance_Monitor parameters on. These monitors can later be removed using the Dihedral/Measure and the Distance/Measure commands.
If you stop a loading process by pressing the <Esc> key, the conformers loaded before the time of the interruption are kept.
Note that, to optimize performance, the torsions are not necessarily searched in the order in which they were input. The order of conformations in the results reflects the search order rather than the input order.
The Vector_Map pulldown contains commands that allow you to create vector maps.
Vector_Map Pulldown
Create
The Vector_Map/Create command allows you to create a vector map by specifying a name and a pair of atoms. A trajectory must be loaded before a vector map can be created.
Color
The Vector_Map/Color command is used to change the color of a vector map's vectors and label.
Label
The Vector_Map/Label command is used to add, move, and remove vector map labels. The label is the name of the vector map.
Display_Vector
The Vector_Map/Display_Vector command is used to blank or unblank individual vectors in the vector map.
List
The Vector_Map/List command is used to report information about the vector map. Various levels of detail are possible.
The Conformer pulldown contains one command, Display, that allows you to derive lists of conformations, perform boolean operations on the list of conformations, and display the conformations in the lists.
Conformer Pulldown
Display
The Conformer/Display command is used to display conformations in the currently loaded trajectory associated with vector maps and graphs.
The Distance_Map pulldown contains commands that allow you to perform boolean operations on distance maps, and to construct distance map graphs either interactively or from a systematic search run with distance map.
Distance_Map Pulldown
Boolean
The Distance_Map/Boolean command allows you to perform a number of different boolean operations on distance maps. The distance maps used must have the same number of dimensions, although the dimensions can be mapped in any order. Corresponding distances in the distance maps must also have the same resolution and bin boundaries.
Construct_Graph
The Distance_Map/Construct_Graph command allows you to visualize distance map data. Up to 3 dimensions of an N-dimensional distance map can be visualized at a time. This is done by projecting any dimension of an N-dimensional distance onto the X, Y, or Z axes of a graph.
Please see the Insight II User Guide for detailed information on this pulldown.
Spreadsheet Pulldown
Please see the Insight II User Guide for detailed information on this pulldown.
Graph Pulldown
Please see the Insight II User Guide for detailed information on this pulldown.
Background_Job Pulldown