QUANTA 2006 includes an interface to features of the CNX program for crystallographic calculations. The main features are:
To access the CNX interface, go to the Applications menu (or enter cnx on the command line prompt).
In addition, two utility programs are accessible from the CNX interface or from the command line by typing cnx util:
For additional information on CNX, please see the CNX documentation and tutorials, which are published separately by Accelrys.
Using tools on the CNX Interface palette, you can set up protocols from QUANTA for CNX, generate CNX scripts, and run CNX calculations. Multiple protocols can be set up, but usually only one can be run at a time on a single host. By using different hosts, you can process multiple CNX jobs simultaneously.
QUANTA manages the files needed to execute a CNX job: an input script containing CNX commands; a reflection file (.cv); and the coordinate file (PDB), PSF file, and parameter file necessary to define the molecular system. The input script is constructed by QUANTA from template files (maps.cnx or refine.cnx) taken from the following directories in order of priority:
This allows the user or group to maintain their own refinement and map calculation protocols. The template files contain all the instructions necessary for running a particular type of calculation. Lines that need to be replaced by QUANTA parameters are labeled with {Q??> } in the first 6 columns.
The initial part of the CNX script defines all the parameters and files to be used in the calculations. The interface can produce a file describing the topology of the molecule (named filename.xpsf) and a parameter file (named filename.xprm), where filename is taken from the name of the first msf in use in the program.
Space group and unit cell dimensions may be obtained by QUANTA while importing a PDB-format coordinate file containing the CRYST1 card, or may be defined by using this tool. This information is necessary for any crystallographic calculations. In using this tool, you are prompted for space group, unit cell information and orthogonalization code. The orthogonalization code defines how the crystallographic coordinate frame is related to the orthogonal coordinate frame used for atomic coordinates. The appropriate value is usually 1.
A file of observed structure factors (Fobs) is required for all CNX calculations. This file must be in CNX format (.cv) and include a complete header and the definition of a test set.
The Set-up Structure Factors tool displays a File Librarian from which to select a reflection file. You also need to define the resolution limits of the data to be used in the CNX calculations.
The Parameter Set tool opens a dialog box for specifying which parameter set to use with CNX. The choices are the standard set of parameters, the Engh and Huber parameter set, or a combined set.
Engh and Huber developed a set of parameters for use in crystal structure refinement following an analysis of the geometry of a series of molecules in the Cambridge Data Base (Engh and Huber 1991). A set of parameters and topology files based on their work has been an integral part of CNX for some time (the parhcsdx.pro and tophcsdx.pro files). The standard parameter set is based on the CHARMm forcefield. Engh and Huber parameters are the more frequently used of the two for refinement.
Specify the desired parameter set with the Parameter Set tool on the CNX Interface palette. You can use QUANTA to construct PSF and parameter files that conform to either the standard or the Engh and Huber parameter set with the Generate CNX PSF command. If the Engh and Huber parameter set is selected, then when PSF generation is requested the following occurs:
1. The current CHARMm parameter file and QUANTA dictionary file settings are saved.
2. The current QUANTA dictionary file is changed to $HYD_LIB/ ehxplor.dic. This maps from the standard protein atom and residue names to the Engh and Huber atom types as defined in the tophcsdx.pro file.
3. The current parameter file, to be used in generating a parameter file from QUANTA, is set to the file $QNT_XRAY/EHXPL.PRM. This contains the Engh and Huber parameter set from parhcsdx.pro converted into a format acceptable to QUANTA.
4. The current set of active atoms is passed to the PSF and parameter generator. The $QNT_XRAY/eh_defs.list file is used to describe the torsions for the named residues. This overrides the generation of all possible torsions, which is the normal output of the PSF generator when generating CHARMm psf files. The parameter chooser asks you to supply any missing parameters.
5. The QUANTA dictionary file and CHARMm parameter file revert to those saved in Step 1.
In this way, the limited set of Engh and Huber parameters is used as a basis for the parameter chooser.
Through the CNX interface, you can specify the essential variables to be used in map generation. The program uses those values to fill in the appropriate fields in the maps.cnx file in the $QNT_XRAY directory. You can set your own protocol for these calculations by changing these files. The program first looks in the working directory for the named files, then in the $QNT_USR area, and finally in the $QNT_XRAY directory.
Clicking Map Generation opens a dialog box in which you can choose:
Tools in the dialog box, and their functions, include:
Omit Residues from Map Calculation Modify the segments and residues used in calculating a map. By default, all atoms in the molecule are selected for map calculations. This can be modified by omitting certain segments or residues.
Residues Enter a residue or residue range.
Define Extent of Map Determine map boundaries, which can be specified in four different ways, following standard CNX usage. The map is calculated to cover the specified volume.
Cover Entire Molecule Calculate a map to cover all atoms in the molecule, with an extra extension (cushion) of 2 Å.
Cover Selected Atoms Calculate a map to cover all displayed atoms, with an extra extension (cushion) of 2 Å.
Fill Unit Cell Calculate a map to fill the entire unit cell.
Fill Defined Box Calculate a map to fill a rectangular volume. The center of the box is defined as the center of rotation of the screen. The box dimensions are arranged around that center. The x, y, and z values of each edge of the box are in Ångstroms.
You provide the essential parameters to be used in rigid body refinement. The program uses them to fill in the appropriate fields in the rigid.cnx file in the $QNT_XRAY directory. You can set your own protocol for these calculations by changing these files. The program first looks in the working directory for the named files, then in the $QNT_USR area, and finally in the $QNT_XRAY directory.
Clicking the Rigid Body Refinement tool opens a dialog box allowing you to set up the refinement protocol. The options are:
You provide the essential parameters to be used in refinement. The program uses them to fill in the appropriate fields in the refine.cnx file in the $QNT_XRAY directory. You can set your own protocol for these calculations by changing these files. The program first looks in the working directory for the named files, then in the $QNT_USR area, and finally in the $QNT_XRAY directory.
Clicking the Refine Structure tool opens a dialog box allowing you to set up the refinement protocol. The options are:
Generate CNX PSF. Generate a PSF and parameter file for the currently selected molecular system.
Set CNX Host... Open a dialog box for selecting an external host on which CNX has been installed and which has been referenced in the file $HYD_LIB/applcomm.db. The $HYD_EXE/cnx.bat file contains the commands to run CNX on an external host. This file must be located on the selected host.
Run CNX... Open a dialog box for selecting an already-existing CNX script to run.
Check Log File Open the Choose CNX log file File Librarian. The selected log file is scanned for errors that may have halted or affected the CNX run and reports any errors to the textport.
Update Coordinates Open the Choose the PDB file File Librarian. After an CNX job is complete, a new set of coordinates is saved in CNX PDB file format. This tool reads those coordinates and updates the current molecular system.
CNX Utilities. Access the CNX utilities described at the beginning of this chapter.
Exit CNX Interface. Close the CNX Interface palette and return to QUANTA core functions.
The alternative location indicator is held for each atom in QUANTA as a (mostly) hidden part of the atom name. It is blank if there is no disorder. Up to six alternative positions are handled by most of the electron density fitting functionality. When a CNX-format PSF or PDB file is saved, this information is queried so that the correct information is included. In addition, PSF generation includes a valence-checking function that ignores atoms that are not disordered but are connected to disordered atoms. PSF generation correctly replicates the bonding as it appears on the screen.