Search_Compare

5       Methodology

This section is a general description of how to use the Search_Compare module. The on-line help (accessed by clicking the ? icon), contains further details about what individual commands and parameters do, and Chapter 6, Tutorial, shows examples of their use.

Using the Volume Pulldown

Objects can be aligned by using the Overlap pulldown in the Search_Compare module, using the Transform/Move or Transform/Superimpose commands from the upper menu bar, or connecting to one of the objects in order to orient it with the dials or mouse.

The Volume/Align command can be used to realign a volume with its reference molecule. The volume that the command is applied to is specified by the Volume Name parameter, and the Reference Molecule parameter indicates the molecule to which the coordinate system of the volume will be aligned.

Specifying How Volumes will be Calculated

The Grid Style parameter determines the extent of the grid, that is, the amount of space in the Insight II "world" occupied by the grid. Setting Grid Style to Enclosure instructs Insight II to automatically determine the extent of the grid needed to enclose the operands. When Grid Style is set to Extents, you can define the Lower Bounds and Upper Bounds (i.e., the two diagonally opposite corners) of the cubic space occupied by the grid, by filling in the X, Y, and Z coordinates of those points. Setting Object_Coords to off means that these coordinates are specified according to the Insight II program's world axes. When Object_Coords is on, these bounds are interpreted in the coordinate space of the object specified by Reference Object. Please refer to the Insight II documentation for a discussion of "world" and "object" space coordinates.

The Border Space parameter specifies the border (in angstroms) that is added around the grid, and the grid resolution (also in angstroms) is specified by the Grid Step parameter. The border should generally be twice the grid resolution, to allow the algorithm to function properly.

Creating Volumes

The name of the object for which the volume will be calculated is supplied to the Operand Name parameter. You may pick a molecule from the Insight II screen, choose a desired operand from the Operand Name value-aid, or enter its name by typing in the Operand Name parameter box. If you type in a molecule name, it may contain wild card characters (*). If it does, the molecules specified are placed in an assembly, and the first molecule name to resolve from the wild card becomes the reference molecule. Then the command executes as if the Volume Level had been set to Assembly.

If a volume is to be created for a molecule, no other parameters must be set before going on to calculate the volume. However, if you want to change the default volume size or specify how to display it (see page 3), you should do so before filling in the Operand Name by picking a molecule or its name, since this is a trigger parameter, meaning that the command executes automatically after it is filled in.

If a volume is to be created from an Assembly, you must specify both an Operand Name (i.e., the name of the assembly) and a Reference Molecule. The coordinate system of the reference molecule is used for the new volume.

For a volume to be created from a Trajectory, the trajectory must first be loaded by using the SC_Search/Load command in the Search_Compare module or the Trajectory/Get command in the Analysis or DeCipher modules. The coordinates of the molecule or assembly to which the trajectory belongs will be updated to match the coordinates of the first frame of the trajectory if the Update_Mol_Coords parameter is on. This can be useful for preventing misalignment between the trajectory and the molecule or assembly. The Atom Move Tol value specifies a minimum distance that an atom must move before its new position is factored into the volume calculation. If the Frame_Range parameter is on, the trajectory frames to be included in the volume calculation are specified with the Start, Last, and Step parameters. If the Frame_Range parameter is off, the trajectory frames are specified in the Frame Spec parameter as a single number (n) or a range of numbers (n-m, >n, <n, >=n, or <=n, where n and m are integers).

Specifying the Volume's Size

Setting Whether and How a Volume Is Displayed

Calculating the Volume

Applying Volume/Create to a molecule results in calculation of the molecular volume and, optionally, display of the volume contour around the molecule. The molecule and volume are automatically associated into an assembly, and a linkage is created between the molecule and its volume. This means that if you connect to and move either the molecule or its volume, the other member of the linkage also moves. The linkage is imposed in order to maintain alignment between the molecule and volume. You can remove an object from the linkage with the Assembly/Remove command.

Applying the Volume/Create command to an assembly results in calculation of the union volume of the molecules in the assembly and, optionally, display of the volume contour around the assembly. The new volume is added to the operand assembly, and a linkage, as described above, is created between the molecules and the volume.

Applying the Volume/Create command to a trajectory results in calculation of the union volume for the conformations in the trajectory and, optionally, display of the volume contour around the molecule to which the trajectory belongs. The molecule and its volume are automatically associated into an assembly, and a linkage, as described above, is created between the molecule and the volume.

Displaying Information About the Volume

The Volume/List command can also be used to report the volume (in cubic angstroms) occupied by an existing volume and the resolution of its grid. If the Output_File parameter is on, this information is written to the file specified by the File Name. If Output_File is off, the volume is displayed in the textport. After you are finished examining the information, you can put the textport away by selecting Textport off at the bottom of the Insight II window.

Boolean Operations on Volumes

To choose which Boolean operation to perform, you need to set the Boolean Operation parameter to Union, Intersection, Difference, or XOR (exclusive-"or"). The results of volumetric operations are also volumes. The union volume is the sum of the operand volumes. The intersection volume is the part of the operand volumes that is common to both operands. The difference volume is the part of a given operand volume that is not shared by a second operand volume. The XOR volume is the part of the operand volumes that is contained in one operand or the other, but not in both.

Before executing the command, you may want to set several other parameters: the Make_Contour, Create_Solids, VDW Scale, and VDW Increment parameters function exactly as in the Volume/Create command (see page page 3). You can also control how many volumes will remain in the display area after the Boolean operation is executed (see below).

The name for a new volume created by a Boolean operation is specified by New Volume Name. This new volume can be added to any of the assemblies to which the operands belong, or a new assembly can be created, as desired, by appropriately setting the Assembly Name parameter. To maintain alignment, a linkage, as described above, is created between the new volume and the operand volumes. Once the Boolean operation is complete, the size of the new volume in cubic angstroms appears in the information area, and the dials are connected to the assembly to which the volume belongs.

Determining How Many Volumes Are Displayed after a Boolean Operation

A volume can also be removed after it is created, with the Object/Delete command on the upper menu bar.

Changing How Existing Volumes Are Displayed

• A line contour (toggle the Contour parameter on and set Solid_Contour to off).

• A point cloud representation of all on grid points (toggle the Point_Cloud parameter on).

• A solid contour (toggle both the Contour parameter and the Solid_Contour parameter on--the Flip_Normals option changes which side of the solid contour is lit).

You can use the Volume/Label command to:

• Label a volume (set Remove to off and set the desired Position Option and Volume Name).

• Change the position of a label (set Remove to off and set the desired Position Option and Volume Name).

• Remove a label (set Remove to on and input the Volume Name).

You can use the Volume/Color command to change the color of a volume's Contour, Point_Cloud, or Label. The Color parameter is easiest to fill in by picking a color from the right side of the Palette value-aid or by mixing a custom color with the sliders on the left side and then accepting it by choosing the block above the sliders.

The commands in the Object pulldown can also be applied to volumes.

Cancelling a Volume Calculation

Using the Overlap Pulldown

To perform molecular similarity calculation/optimization, specify the molecule to use by defining one atom pair between two molecules. Then start the calculation using the Field_Fit command.

Using Highlights

To specify these highlight options, you select the Overlap/Display command. You then turn atomic labels, link highlights, and torsion highlights on or off by toggling the Display_Label, Display_Link, and Display_Torsion parameters.

These highlights can be turned on or off at any time. If the highlights are turned on, they remain on either until they are turned off explicitly or until the overlap specifications are deleted (they may also be deleted indirectly through deletion of the molecules).

Defining Atom Pairs

You specify these atom pairs with the Overlap/Define command, by setting Definition Action to Add, choosing Atoms as the Definition Type, setting the Define Pick Level to Atom, and supplying the names of the two atoms to be superimposed. This is done by picking atoms in the molecules in the display area, to fill in the Overlap Spec 1 and Overlap Spec 2 parameters. Each atom must belong to a different molecule.

You may also specify two groups of atoms to be superimposed simultaneously. The group of atoms may be atoms in a molecule, a subset, or a monomer/residue. In this case, the numbers of atoms in the two groups must be the same, and the atoms are paired automatically by Insight II according to the internal sequence. To do this, you again set the Definition Action to Add and the Definition Type to Atoms. But now you set Define Pick Level to Molecule, Subset, or Monomer/Residue. You then pick atoms in the molecule as before, to fill in the Overlap Spec 1 and Overlap Spec 2 parameters. You should always verify that the automatic specifications are what you expected (see Checking the Specifications).

Note that you can define atom pairs among several molecules, if you want to superimpose more than two molecules. For example, if you want to superimpose atom p in molecule A, atom q in molecule B, and atom r in molecule C on one another, you only need to define the p-q and q-r atom pairs.

Wildcards are allowed for Overlap Spec 1 and Overlap Spec 2, but the atoms specified by Overlap Spec 1 must be in the same molecule. Overlap Spec 2 may specify atoms from a different molecule, as long as the numbers of specified atoms in each molecule are the same.

These atom pair specifications remain in the memory throughout the Insight II session. You can modify them by adding or deleting at any time. However, they cannot be saved or restored using a file.

Setting Up Torsions

To specify rotatable bonds, you need to set the Definition Action to Add and the Definition Type to Torsion. You may specify a) one bond or b) a group of bonds at a time, by setting the Define Pick Level parameter to a) Atom or b) Molecule, Subset, or Monomer/Residue, as desired. In specifying one bond, you need to supply the names of the two atoms forming the rotatable bond, by picking atoms in the molecule in the display area. This fills in the Overlap Spec 1 and Overlap Spec 2 parameters. In specifying a group of bonds at once, you only need to specify the name of the molecule, subset, or monomer/residue as Overlap Spec 1 (again by picking), and all rotatable bonds are automatically added to the specification. You may use wildcards in Overlap Spec 1 and Overlap Spec 2 to specify a group of bonds.

These torsion specifications remain in the memory throughout the Insight II session. You can modify them by adding or deleting at any time.

Checking the Specifications

Correcting Mistaken Entries

Specifications of individual rotatable bonds are removed in the same way, except that the Definition Type is set to Torsion and the Deletion Mode is not used. To remove all rotatable bond specifications pertaining to a group of atoms, set the Define Pick Level to Molecule, Subset, or Monomer/Residue and pick one atom in the molecule, subset, or monomer/residue.

To remove all atom pair specifications that relate directly to a given atom (links), set the Deletion Mode to Atoms and fill in only Overlap Spec 1, by picking that atom on the screen. To remove specifications for all atoms that are linked (directly or indirectly) to a given atom, set the Deletion Mode to Chains before picking the atom.

To remove all specifications for atom pairs or rotatable bonds, set the Definition Action to Clear and set the Definition Type to Atoms or Torsion.

You then change the Definition Action back to Add to input any specifications that are still needed, as explained above.

Executing the RMS Fitting Calculation

Before you execute the command to start the calculation, you may want to set three optional features first, to cause the superimposed molecules to be displayed in different colors and (or) to all be associated into an assembly. Toggling the Color_By_Molecule parameter on helps you to distinguish the molecules after they are superimposed. Toggling the Form_Assembly parameter on and entering a name for the Assembly Name parameter allows you to rotate or move them all together. Toggling the Create_Table parameter to on enables you to create a table listing RMS values between each pair of molecules.

Executing the command then starts the overlap calculation.

After the calculation finishes, all molecules are automatically aligned on the screen, and the final value of the rms difference between their atomic coordinates is displayed in the information area.

Executing the Field Fitting Calculation

There are two types of calculations you can perform. The first type calculates the field similarity using the molecules' current position. You start this calculation by toggling the Optimize_Fit parameter off and selecting Execute. You may also move the molecules using the mouse and then execute the command to monitor the similarity. In addition, you can toggle the Create_Table parameter on and fill in the Table Name parameter to create a table listing the similarities between each pair of molecules.

The second type of calculation optimizes the similarity by moving the molecules (molecular translation, molecular rotation, and torsion rotation). You start the calculation by toggling the Optimize_Fit parameter on and selecting Execute.

There are several optional features you may select. The Pre_Align parameter specifies whether to align molecules using their dipole moments and quadrupole moments to the best starting position, or to simply use the current position as the starting position for the optimization.

Toggling the Color_By_Molecule parameter on helps you to distinguish the molecules after they are superimposed. Toggling the Form_Assembly parameter on and entering a name for the Assembly Name parameter allows you to rotate or move them all together. Toggling the Create_Table parameter on and entering a name for the Table Name parameter creates a table detailing the similarities between each pair of molecules. The overall similarity is also listed (in the upper left corner cell).

Using the SC_Search Pulldown

Systematic conformational searching runs as a background job. Insight II is used to set up and initiate the background job and, when the job completes, to load the search results for viewing and analysis. Two pulldowns are used in conformational searching: the SC_Search pulldown is used to set up search parameters, initiate the background job, and load the search results; and the Background_Job pulldown is used to set up background job parameters and monitor the job as it runs.

The systematic conformational search procedure consists of four steps:

1.   Setting up parameters for the search and the background job.

2.   Running the background job.

3.   Preparing the results for analysis.

4.   Analyzing the search results.

The second step is accomplished by executing the SC_Search/SCS_Run command, which creates a command file containing specified information that was set up in Step 1 and submits it to the searching program. You can check on the status of the background job with the Background_Job/Completion_Status command. The searching program runs in the background and notifies you when it is finished.

The third step is accomplished in several ways. Executing the SC_Search/Load command loads the search results into Insight II in the form of a trajectory. You may set up runs that use or refine the results of an earlier search, which involves reiterating steps one and two.

The fourth step depends on your particular purpose for generating conformations. The commands in the Vector_Map pulldown, Distance_Map pulldown, Conformer pulldown, and the Analysis or DeCipher modules are useful for analyzing the results of systematic conformational searches.

The first three steps are presented in detail below. Each of the SC_Search and Background_Job commands and parameters is explained. Standard search procedures are presented in the first section, and searches involving the creation or use of distance maps and energy criteria follow in a separate section.

Standard Searches

Defining the Bonds to be Rotated

To read rotatable bonds from a prior input file, you need to set Rot Bond Mode to Prior_Input and specify the File Name (search parameter files have the extension .scs_prm). Then fill in the Molecule Name by picking the molecule in the graphics area of the screen, choosing its name from the Molecule Name value-aid, or typing in the Insight II name of the molecule containing the rotatable bonds.

To specify rotatable bonds interactively, set Rot Bond Mode to User_Defined. Several other pieces of information are needed: the two atoms defining the rotatable bond (Atom 1 and Atom 2); the Range (in degrees relative to the current dihedral angle of the bond you want to rotate--Relative_Range must be on); and the Increment for stepping through the range (also in degrees). Alternatively, you can define a particular dihedral by toggling Relative_Range parameter off and specifying the four atoms that define the dihedral (the parameters Atom 1, Atom 2, Atom 3, and Atom 4). In this case, you specify, following the IUPAC convention, the Range of absolute dihedral angle values (in degrees) through which to search and the Increment. Continue adding definitions in the same manner until all desired rotatable bonds are specified.

Wildcards can be used to define a group of torsions in one command execution. To do this, toggle the Relative_Range parameter to on, and specify the torsions using the Atom 1 and Atom 2 parameters. This adds all valid single bonds (including ring bonds) specified by the two parameters. For example, if you type

>	MOL:*:CA

>	MOL:*:*

You can remove rotatable bonds from the list by setting the Rot Bond Operation parameter to Delete, specifying the two atoms of the rotatable bond (the Atom 1 and Atom 2 parameters), and executing the command. You can remove all rotatable bonds from the list by setting the Rot Bond Operation parameter to Clear and executing the command.

You can review the current list of rotatable bonds by setting the Rot Bond Operation parameter to List and executing. After examining the information in the textport that appears, you can put away the textport by selecting the Textport off at the bottom of the Insight II window.

Scaling Atomic Radii

Setting Distance Constraints

• By setting the Distance Mode parameter to Prior_Input and reading in a set of distance constraints from the parameter file of a previous search.

• By setting the Distance Mode parameter to Prior_Output and deriving distance constraints from the results of a previous search.

• By setting the Distance Mode parameter to User_Defined and specifying the atoms and bounds for each distance constraint.

To read distance constraints from a Prior_Output file, you specify the File Name (of an .scs_tor or .xdr_tor file), the two atoms whose interatomic distance you want to constrain (the Atom 1 and Atom 2 parameters), and the two atoms of the previous search (these need not be from the same molecule) whose longest and shortest interatomic distances should become the upper and lower bounds of the new distance constraint (the Prior Search Atom 1 and Prior Search Atom 2 parameters). The minimum value of their distance during the previous search becomes the lower bound, and the maximum value of their distance becomes the upper bound. If the Interactive_Calc parameter is on, the bounds are calculated immediately and printed in the information area. If
Interactive_Calc is off, the bounds calculation is deferred until the search job is initiated.

To enter distance constraints in the User_Defined mode, you specify the two atoms whose interatomic distance you want to constrain (Atom 1 and Atom 2) and the Lower and Upper bounds of acceptable values for the distance (in angstroms).

You can remove a distance from the list by setting the Distance Operation parameter to Delete and specifying the two atoms (Atom 1 and Atom 2) to remove from the list. Setting the Distance Operation parameter to Clear removes all distance constraints from the list.

You can review the current list of distance constraints by setting the Distance
Operation parameter to List. After examining the information in the textport that appears, you can put away the textport by selecting Textport off at the bottom of the Insight II window.

Setting Up the Background Job

When the Setup_Bkgd_Job command is used, the background job list shows only those background jobs that are both run from the current module and can be run on a remote host. If the module contains only one job, the parameter is automatically filled in. The list of hosts shows only those hosts that are associated with that background job in the background_job_hosts file at your site. It is possible for you to specify a remote host that is unavailable (off line, for instance) or for which you have no login account.

Every background job submitted via the generic background utility is assigned a job number. This number is displayed in the information area when the job is submitted (e.g., Starting systematic search job on iris5 as job 1). You should note the job number when the job is submitted, since it can be used later to check on the job's completion status or to kill the job.

The Setup_Bkgd_Job command does not actually run the command; it simply records your host and Execution_Mode preference. The default host is Local. Your selected host and Execution_Mode are used for any subsequent background jobs of the specified program for the duration of the Insight II session. When you start up a new session, all background job parameters are reset to their default values.

The Execution_Mode parameter allows you to choose to run a given background job concurrently (Cont_Insight), run the job interactively (Wait_For_Job), or simply create the necessary command files to submit the job, but not actually execute them (Cmd_File_Only).

The Send_Mail parameter instructs the system to send you an electronic mail message upon completion of the background job. This parameter is not active if Execution_Mode is set to Wait_For_Job. You may find Send_Mail useful when running long jobs where you exit Insight II before the job completes.

The Save_Cmd_Files parameter allows you to save the command file used to submit the background job (bkgd_job_run_name#.csh). Otherwise this file is deleted when the job completes. This parameter is not active when Execution_Mode is set to Cmd_File_Only.

All background jobs return a completion status. The completion status is an integer code that indicates success, failure, and/or reason for failure of the job. The status code is always displayed when you are notified that the job has completed.

If you consistently want to send background jobs to another host, you can modify your personal Insight II start-up file to invoke Setup_Bkgd_Job for each module/background job(s) that you want to automatically assign. Note that you must first change to the module in which the background job's interface is found before using Setup_Bkgd_Job to set a preference for that background job.

The Completion_Window parameter can be used to prevent the notification window from appearing when the background job completes. The default setting is on.

Running the Background Job for Standard Searches

To estimate the number of conformations that will be obtained with a particular set of parameters before actually performing the search, set Estim_Num_Confs to on. The estimate takes into account all the currently defined parameters applicable to the molecule specified in Molecule Name. However, no search is initiated.

To initiate a standard search, turn Estim_Num_Confs to off and set Search Type to Standard. You need to specify the molecule on which you want to perform a search (the Molecule Name parameter), and rotatable bonds must have been defined for that molecule before a search can be performed. Existing distance constraints and scaling factors are taken into account in the search calculations.

In addition to Search Type, you can set the Search Method parameter, which may be set to one of two values. Setting this to Torsion_Search indicates the search molecule will be used to generate a new set of conformations from a torsion search that uses the torsions and step values specified by the Set_Rot_Bond command. If the Search Method parameter is set to Prior_Search, the set of initial conformations is taken from an existing trajectory file (XDR_TOR or ARC) for the search molecule. With this setting some of the SCS_Run command parameters are renamed or not available, which reflects the fact that you are running the search to filter or process an existing set of conformations.

By default, a fixed atom (that is, one whose coordinates remain fixed during the calculations) is chosen by the algorithm. However, you may want to choose a specific atom to remain fixed, by specifying it with the Anchor Atom parameter. You also need to supply a Run Name. This name serves as the prefix for all the files generated by the search. Exactly what files are generated depends on the options that are set.

Monitoring the Job

The Report_Mode parameter is used to indicate what information you would like the command to return: status of one job, status of all jobs, or the meaning of a return status code from a particular job.

The Job_Number parameter becomes active when One_Job is selected. It is used to specify a specific background job that you want to monitor.

The Background_Job and Status parameters become active when Look_Up_Status is chosen. They are used to specify a status code that you would like to look up.

Killing a Background Job

The Job_Number parameter is used to specify which background job to kill. A value-aid containing a list of all currently running background jobs is provided.

If the Save_Output parameter is toggled on, then all output files generated by the background job are saved when the job is killed. The default setting for this parameter is off, in which case all output files are deleted.

Please note that, if you kill a background job and keep the output files, the files contain only the partial results of the searching process.

Loading Search Results into Insight II

You select which file to load with the Torsion File parameter and tell Insight II which molecule the file applies to with the Molecule Name parameter. To load a complete set of search results, set the Selection Mode to Range. The default values for the Trajectory Spec parameters (Start, Last, and Step) should be accepted (1, end, and 1, respectively). To limit the amount of data loaded, you may do one of three things:

• Leave the Selection Mode as Range, but change the values of Start, Last, and/or Step.

• Choose Specified as the Selection Mode, and specify the desired trajectory frames in Frame Spec as a single number (n) or a range of numbers (n-m, >n, <n, >=n, or <=n, where n and m are integers).

• Choose From_File as the Selection Mode, to indicate that the desired frame numbers are specified in an ASCII file (specified as the File Name) that you have created with any editor or by using the Output_list option of the Conformer/Display command (see page 34).

Table 1 summarizes the process of setting parameters for various types of searches using the distance map and energy features.

Table 1

Note that some of these search types cannot be combined, such as distance map creation and energy calculation.

Rotatable bonds, interatomic distance constraints, and radius scaling, as well as background job parameters, are set up exactly as described for the standard searches. You may refer to Setting up Parameters for the Standard Search and Background Job on page 14 for further information on using these commands.

After an advanced search, results are loaded in the same way as they are in standard searches (see above).

Setting up Distance Map Calculations

You set up a new distance map by setting Dist_Map Operation to Add and
Prior_Search_Dmap to off, then specifying the atom pair (the Atom 1 and Atom 2 parameters) that defines one distance, the Lower and Upper bounds for that distance, and the Resolution. Continue defining atom pairs in the same way, until you have as many atom pairs as you want to monitor. Each distance in a distance map may have a different resolution. All distances are in angstroms.

A distance map can also be used as a constraint on a subsequent search, which means that only conformations that map to a valid point in the constraining distance map are accepted. This is particularly useful for identifying common geometries among a series of active compounds. To constrain your distance map to the results of a prior search, set the Prior_Search_Dmap to on. The resolution and bounds for your new map are then derived from the distance map file of a previous search, specified by the Dist_Map File parameter.

When constraining your current map to a prior search map, you must ensure that the constraining distance map and the current map contain the same number of distances. This is accomplished by mapping each distance one-for-one to a distance in the constraining map. The Dist_Num parameter is an index in the constraining distance map file that enables the corresponding distance in the molecule specified by the Source Molecule parameter to be highlighted. You then define the equivalent interatomic distance for the molecule to be constrained, by specifying its two atoms with the Atom 1 and Atom 2 parameters. The Dist_Num counter is then incremented so you can map the next distance, until all distances have been mapped. You can also directly specify a certain distance by setting the Dist_Num parameter to a specific value--provided that it is smaller than the number of distances in the constraining map. A warning is issued upon exiting or canceling the Set_Dist_Map command if all distances have not been mapped.

Note that only one distance map can be defined at a time in an Insight II session. You can remove an existing map by setting the Dist_Map Operation to Clear. You can remove an individual atom-pair distance from the map by setting the Dist_Map Operation to Delete and specifying the atoms in that pair as Atom 1 and Atom 2.

To see a list of the information about the current map, set the Dist_Map Operation to List. After examining the information in the textport that appears, you can put away the textport by selecting Textport off at the bottom of the Insight II window.

Setting up Energy Calculations

Very often, instead of wanting to see all possible conformers that are sterically allowed and satisfy certain distance constraints, you may be interested in finding only a small number of conformers that are energetically most stable. The Max Conformers parameter allows you to specify the maximum number of the most stable conformers to keep.

Additionally, an energy threshold can be specified for screening out those conformers whose energy values are the specified amount above the minimum energy (i.e., the energy value of the most stable conformer among all conformers that have passed checking for steric clashing and that satisfy the distance constraints). You specify this threshold by filling in the Energy Threshold parameter (in kcal mol^-1).

The Max Conformer and Energy Threshold parameters are used together to decide the actual number of conformers to keep.

Next, you need to specify whether to simply calculate the energy or to minimize the energy for each conformer. In the former case, the total energy is calculated for the conformers that have passed checking for steric clashes and that satisfy the distance constraints. These conformers are generated by strictly rigid rotation of the torsions you specified with the Set_Rot_Bond command. You specify simple calculation of energy by toggling the Optimize parameter off.

If, on the other hand, your goal is to find a set of minimized conformers that are the most stable, you toggle the Optimize parameter on. In this case, the conformers that have passed checking for van der Waals clashes and that satisfy the distance constraints are minimized. Please see Use of Energy Criteria in Systematic Conformational Searching, in Chapter 3 of this User Guide, as well as the Discover documentation, for information on how the minimization is performed.

If you toggle the Optimize parameter on, you must specify three more parameters:

1.   The maximum number of iterations used in the minimization process is set with the Iterations parameter. This prevents the calculation from continuing for an inordinately long time.

2.   The maximum allowable derivative at which the minimization process stops (i.e., the convergence criterion) is set with the Derivative parameter.

Note that minimization can take a long time. You can reduce this time by setting the Iterations parameter to a smaller number and the Derivative parameter to a larger number.

3.   Whether or not duplicate removal occurs for any search type, including Energy, is controlled via the Set_Filter_Params command. Here you may specify whether duplicates are removed, if symmetry is considered, the threshold values for the RMS and Energy comparisons made to identify duplicates, and the set of atoms used for identifying duplicates (the default is to use only the heavy atoms and polar hydrogen atoms). However, there is one duplicate removal parameter that is specific to optimized searches, Prescreen_Dupl. When set (the default condition) this instructs the search to perform duplicate removal twice: once on the torsional conformations prior to optimization and then again after the optimization. This parameter will not affect the results of the search but can significantly improve the overall search time, especially for molecules that contain local symmetry, by filtering before the optimization and thereby reducing the number of conformations that need to be minimized.

Executing the Set_Energy_Params command does not start the calculation. Instead, the specified parameters are stored internally and are used when you execute the SCS_Run command with the Search Type parameter set to Energy.

Initiating the Background Job for Advanced Searches

To estimate the number of conformations that will be obtained with a particular set of parameters before actually performing the search, set Estim_Num_Confs to on. The estimate takes into account all the currently defined parameters applicable to the molecule specified in Molecule Name. If a constraining distance map has been specified, the lower and upper bounds of each distance in the map are accounted for. The estimate indicates the maximum possible number of conformations that might be found. However, some conformations will be screened out during the search. No search is initiated.

To initiate a search, turn Estim_Num_Confs to off. You need to specify the molecule on which you want to perform a search (the Molecule Name parameter), and rotatable bonds must have been defined for that molecule before a search can be performed. Existing distance constraints (but not distance maps--see Table 1) and scaling factors are also taken into account in the search calculations. To have distance map criteria taken into account, set Search Type to Dist_Map. To have energy criteria used, set Search Type to Energy. Energy computations significantly increase the time needed to perform the search.

You can combine distance constraints with distance map creation or distance map constraints. However, distance map and energy calculations cannot be performed in a single search run, to avoid inconsistencies between the generated conformers and the distance map. Thus, if a current distance map definition exists for the molecule on which a search with energy calculation is requested, the distance map is ignored and energy calculations are performed.

When initiating a search, you also need to supply a name with the Run Name parameter. This name serves as the prefix for all the files generated by the search. Exactly what files are generated depends on the options that are set (for example, distance map files, archive files, torsion files). The run name is also used to generate the files that are required for input to the search background job--the .car, .mdf, and .scs_prm files.

By default for any search performed, a fixed atom (whose coordinates remain fixed during the calculations) is chosen by the algorithm. However, you may want to choose a specific atom to remain fixed, by specifying it with the Anchor Atom parameter. Note that if the specified anchor atom does not belong to the subset of atoms that contain the defined interatomic distances, then the distance map calculations ignore this anchor atom and pick another one. In this case, a message is printed in the <run_name>.scs_log file produced by the search background job.

When Search Type is set to Dist_Map, a distance map output file is always produced. If you have defined a prior distance map as a constraint for the search using the Set_Dist_Map command with Prior_Search_Dmap set to on, then the search uses it as a constraint.

If you only want to create a new distance map based on the map defined with the Set_Dist_Map command (without producing any conformations), set Create_DMap_Only to on in the SCS_Run parameter block.

To combine energy calculations with a search, set Search Type to Energy. Energies--either single-point calculations or optimizations, depending on the settings previously defined with Set_Energy_Params--are calculated for each generated conformer after verifying that the conformer meets all other criteria and standard distance constraints. To optimize this type of search and ensure that the current conformation is included as one of the final conformers, you should minimize the molecule before initiating any search.

You can also post-process the results of a search by setting Search Method parameter to Prior Search. Initial conformations will then be taken from the trajectory file specified by the Input File parameter.

There are essentially three processing methods that may be selected using the Prior_Search Filter parameter. When set to RMS_Only, the new set of conformations will have been re-filtered for duplicates, using your current duplicate removal parameters. When set to RMS_And_Energy, the new set of conformations will be re-filtered for duplicates and will have energies (re-) calculated for each conformation. When set to Dist_Map, a distance map file will be produced for the conformations. If a prior distance map file was also specified through the Set_Dist_Map command, then the conformations will also be filtered to those which conform to one of the distance map points in this file. This is like filtering with a specific set of narrow distance constraints and is the method by which common distance maps can be determined for a set of different molecules.

Note: The Molecule Name parameter is only required for Dist_Map prior searches since for RMS/Energy filtering the molecule is implied by the trajectory file. However, the molecule name is required if you wish to use a user-defined set of RMS atoms for duplicate removal since this specification is a property of the molecules currently in Insight II.

Using the Distance_Map Pulldown

Boolean operations use two distance map files (the Ref Dist Map File and the Op Dist Map File) as input, and yield a single new distance map file (the Output Dist Map) as output.

To perform a boolean on two distance map files, the following must be true:

1.   The number of distance definitions for the two distance map files must be equal.

2.   The resolution of corresponding distance definitions between the two distance map files must be equal (this correspondence is further discussed below).

3.   The lower bound of corresponding distance definitions between the two distance map files may only differ by integer multiples of their resolution.

N = ...-2,-1,0,1,2,...

The correspondence of distance definitions associates each distance definition of the reference distance map file (Ref Dist Map File) uniquely to a distance definition in the operand distance map file (Op Dist Map File).

In the case of performing boolean operations on distance map files, each with two distance definitions, you can define the correspondence by associating the first distance definition in the reference with the first distance definition in the operand, and the second distance definition in the reference with the second definition in the operand. Alternatively, you may associate the first distance definition in the reference with the second distance definition in the operand, and the second distance definition in the reference with the first distance definition in the operand. Each distance definition must be associated with a distance definition in the other file.

The Output Dist Map file contains the distance definitions from the Ref Dist Map File, and the result of the boolean operation of the distance map points in the two files.

Setting up a Boolean Distance Map Calculation

To set up a user defined correspondence, select User_Defined as the Mapping Function. While defining the mapping correspondence, you must specify a Ref Molecule Name associated with the Ref Dist Map File, and an Op Molecule Name associated with the Op Dist Map File. To aid in defining the correspondence, a monitor appears on the reference molecule when you specify a Ref Dist Num distance definition number. Similarly, when you specify an Op Dist Num, a monitor appears on the operand molecule.

Once you have provided a unique association for each distance definition, you must select the End_Definition option of User Defined Map. When executed, the boolean operation is performed using the correspondence you defined.

To clear correspondences you defined, select the Clear option of User Defined Map, and select Execute. To see correspondences you defined, select the List option of User Defined Map, and select Execute.

Visualizing a Distance Map as a Graph

Constructing a Distance Map Graph of an N-Dimensional Distance Map

When constructing a graph from a distance map file, you need to specify a Dist Map File Name, a Ref Molecule Name associated with the Dist Map File Name, an X_Dist_Num, a Y_Dist_Num, and a Z_Dist_Num. The X_Dist_Num is the distance definition number in the Dist Map File Name to be projected onto the X-Axis. The Y_Dist_Num is the distance definition number in the Dist Map File Name to be projected onto the Y-Axis. The Z_Dist_Num is the distance definition number in the Dist Map File Name to be projected onto the Z-Axis. To aid in specifying the desired distance number for each axis, a monitor is displayed on the molecule specified in Ref Molecule Name, which identifies the distance definition in Dist Map File Name.

If the Ref Molecule Name is associated with the currently loaded trajectory, then each graph point will have associations with the appropriate trajectory frames.

Constructing a Distance Map Graph From a Trajectory.

To specify distance definitions from a prior run, select Prior_Output as the Distance Definition. Specify the prior distance map file as the Dist Map File Name, then select the distance definitions to project onto each axis of the graph.

To specify new user defined distance definitions for the distance map graph, select User_Defined as the Distance Definition. Then for each Graph Axis, specify an Atom 1, Atom 2, Lower, Upper, and Resolution.

Using the Vector_Map Pulldown

Before creating a vector map, you must have a molecule present in the Insight II program, and have loaded a trajectory that is associated with that molecule. The trajectory can be obtained with either the Trajectory/Get command in the Analysis module or the SC_Search/Load command in the Search_Compare module.

Creating and Editing a Vector Map

You may view information about the current vector map by selecting the Vector_Map/List command. Input the Vector_Map Name by choosing it from the value-aid, then select the Detail Level you want, by choosing Names, Details, or Extra_Details. The information is output to the textport or to a file, depending on whether Output_File is off or on, respectively. If you have the information output to the textport, you can put away the textport after examining the information in it, by selecting Textport off at the bottom of the Insight II window.

Controlling the Display of a Vector Map

The Vector_Map/Color command is used to change the color of two components of the vector map, by selecting the Vector_Map Name and setting Vmap Attribute to Vectors or Label. The Color parameter is filled in with the help of a Palette value-aid (see Changing How Existing Volumes Are Displayed, page 6, for further information on using this value-aid).

The Vector_Map/Label command is used to add or move (if Remove is off) or to delete (if Remove is on) the vector map label. The position of the labels can be controlled with the Label Position parameter. Choosing Above, Below, Left, or Right places the label in the indicated position relative to the vector map. If you want to place a label at a defined point in space, select Coord and then input the X, Y, and Z Label Coordinates. If you want to place a label on a certain vector, choose On_vector, then fill in the Vector Spec parameter by picking that vector in the display area.

You can hide or display individual vectors in the vector map with the Vector_Map/Display_Vector command. The Blank Operation must be turned On or Off to hide or show, respectively, the vectors specified by Vector Spec. The format for specifying one or more vectors in Vector Spec is the vector map name, followed by a colon (:), followed by a single number (n) or a range of numbers (n-m, >n, <n, >=n, or <=n, where n and m are integers). The easiest ways to specify a single vector are either to pick the vector in the Insight II display area or to choose its name from the value-aid in the parameter block.

Using the Conformer Pulldown

Displaying Desired Conformers

• Choosing Conformer_number as the value of the Display Derivation parameter and entering a valid Conformer Number.

• Choosing List_index as the value of the Display Derivation parameter and selecting an index in the current list by entering a number (1 for the first conformation in the list, 2 for the second, etc.) for the List Index or by moving a scroller in an Index Valuator value-aid.

• Choosing Lowest_energy as the value of the Display Derivation parameter, to show the one conformer in the list that has the lowest energy.

Manipulating the List of Conformers

You can select conformers according to energy criteria by toggling the Energy_screen parameter on and entering an integer for N_Lowest Energy, indicating the number of lowest-energy conformers that you want to retain in the list. This trims the current list so that it contains only the N lowest-energy conformers.

Boolean operations on the lists of conformations associated with vector maps or distance map graphs allow you to visualize conformations where the movements of pairs of atoms are related in certain ways. For example, you might want to see all conformations where a pair of atoms exists in various locations of one vector map, or conformations where a pair of atoms exists in one vector map and where a different pair of atoms exists in another vector map at the same time.

To perform Boolean operations on the existing list, choose Modify_list as the Display Function. In addition, an intermediate list of conformations is needed in order to modify the current list. The List Derivation parameter indicates how this list should be derived:

• You may specify certain frames (and their associated conformers) that you want to use, by choosing Frame_spec as the List Derivation. You then enter the desired frames in the Frame Spec parameter by entering a single frame number (n) or a range of numbers (n-m, >n, <n, >=n, or <=n, where n and m are integers). Blank spaces and tabs are ignored by Insight II.

• You can also obtain the same type of information from a file, by choosing From_file as the List Derivation. You then enter the File Name, which specifies an ASCII file referring to the current trajectory and containing a list of frame number(s) in the same format as above. You either create this file with any text editor or input it from a previous output list.

• Choosing Graph/Vmap as the List Derivation means to select the list of conformations associated with the vectors specified by the Graph/Vmap as the intermediate list of conformations. Picking the vector or graph point in the display area fills in the Graph/Vmap parameter. Be aware, however, that some vector maps and graphs may not have associated frame information--if you make changes to the trajectory or molecule to which a vector map or graph refers, then its frame information is no longer valid.

• Difference, which removes the conformers contained in the intermediate list from the current list;

• Intersection, which generates a new list containing the conformers that were present in both lists;

• Replace, which replaces the current list with the intermediate list;

• Union, which combines the two lists into one; and

• XOR, which generates a list of conformations that are present in either of the two lists but not in both.