################## NCIPLOT Tutorial ################## This section will cover NCIPLOT analysis capabilities in CHEMSMART. .. note:: For NCI visualization using PyMOL, see :doc:`pymol-interaction-analysis`. ********** Overview ********** NCIPLOT is a tool for analyzing non-covalent interactions in molecular systems by generating density and reduced density gradient (RDG) cube files. CHEMSMART provides a convenient interface for running NCIPLOT calculations through the ``chemsmart sub nciplot`` command. ******************************************* Input File Types and Density Calculations ******************************************* NCIPLOT supports different types of input files, and the density calculation method depends on the file format: Promolecular Density ==================== When using structure files without wavefunction data (e.g., ``.xyz``, ``.log``, or other geometry files), NCIPLOT calculates the density using **promolecular approximation**. This method is faster but less accurate than using SCF wavefunction data. **Supported file formats for promolecular density:** - ``.xyz`` - Cartesian coordinates - ``.log`` - Gaussian output files (coordinates only) - Any other geometry file format supported by chemsmart's file converter **Behavior:** When you provide these file types, chemsmart automatically: #. Appends ``_promolecular`` to the job label (unless already present) #. Converts non-XYZ files to XYZ format with ``_promolecular.xyz`` suffix #. Generates output files with the promolecular label Wavefunction Density ==================== When using wavefunction files (e.g., ``.wfn`` or ``.wfx``), NCIPLOT uses the **SCF wavefunction density** for more accurate calculations. **Supported file formats for wavefunction density:** - ``.wfn`` - Gaussian wavefunction file - ``.wfx`` - Extended wavefunction format **Behavior:** When you provide these file types, chemsmart: #. Uses the original file label without modification #. Directly uses the wavefunction data for density calculations #. Generates output files without the promolecular suffix .. warning:: After the required files have been generated with NCIPLOT, they can be loaded using chemsmart's built-in :doc:`PyMOL visualization commands `. However, the same molecular structure may yield different NCI plots depending on whether NCIPLOT uses **promolecular density** or **wavefunction density**. Workflow (Gaussian → NCIPLOT → PyMOL) ===================================== .. code:: text test.log file or test.xyz file | | +-------------------+-------------------+ | | | chemsmart sub gaussian -f test.log nci | | | v v generate test_nci.wfn +-----------------------------------------+---------------------------------------+ | Promolecular (use .log / .xyz) | Wavefunction (from .wfn/ .wfx) | +-----------------------------------------+---------------------------------------+ | test.log | test_nci.wfn | | (or test.xyz) | (or test_nci.wfx) | | | | | | | v | v | | chemsmart sub nciplot -f test.log | chemsmart sub nciplot -f test_nci.wfn | | | | | | | v | v | | test_promolecular-dens.cube | test_nci-dens.cube | | test_promolecular-grad.cube | test_nci-grad.cube | +-----------------------------------------+---------------------------------------+ | v chemsmart run mol -f ... nci | v nci_promolecular_density.pse / nci_wavefunction_density.pse .. raw:: html
NCI plot using Promolecular Density

Promolecular Density

NCI plot using Wavefunction Density

Wavefunction Density

**************** Usage Examples **************** Example 1: Using XYZ File (Promolecular Density) ================================================ .. code:: bash chemsmart sub -s xz nciplot -f azetidine_nci.xyz **What happens:** - Input file: ``azetidine_nci.xyz`` - Job label: ``azetidine_nci_promolecular`` - Input file for NCIPLOT: ``azetidine_nci_promolecular.nci`` - Output files: - ``azetidine_nci_promolecular.nciout`` - ``azetidine_nci_promolecular-dens.cube`` - ``azetidine_nci_promolecular-grad.cube`` Example 2: Using Gaussian Log File (Promolecular Density) ========================================================= .. code:: bash chemsmart sub -s xz nciplot -f azetidine_nci.log **What happens:** - Input file: ``azetidine_nci.log`` - File converted to: ``azetidine_nci_promolecular.xyz`` - Job label: ``azetidine_nci_promolecular`` - Input file for NCIPLOT: ``azetidine_nci_promolecular.nci`` - Output files: - ``azetidine_nci_promolecular.nciout`` - ``azetidine_nci_promolecular-dens.cube`` - ``azetidine_nci_promolecular-grad.cube`` Example 3: Using Wavefunction File (SCF Wavefunction Density) ============================================================= .. code:: bash chemsmart sub -s xz nciplot -f azetidine_nci.wfn **What happens:** - Input file: ``azetidine_nci.wfn`` - Job label: ``azetidine_nci`` (no promolecular suffix) - Input file for NCIPLOT: ``azetidine_nci.nci`` - Output files: - ``azetidine_nci.nciout`` - ``azetidine_nci-dens.cube`` - ``azetidine_nci-grad.cube`` **Important Note:** Even if ``azetidine_nci.wfn`` exists in the same directory, using ``-f azetidine_nci.xyz`` or ``-f azetidine_nci.log`` will still run the job using promolecular density. You must explicitly specify the ``.wfn`` file to use wavefunction density. ******************* Custom Job Labels ******************* You can override the automatic labeling behavior using the ``-l`` or ``--label`` option: .. code:: bash # Custom label for XYZ file chemsmart sub -s xz nciplot -f azetidine_nci.xyz -l my_custom_label **Result:** Job will be labeled ``my_custom_label_promolecular`` (promolecular suffix is still added for non-wavefunction files) .. code:: bash # Custom label for WFN file chemsmart sub -s xz nciplot -f azetidine_nci.wfn -l my_custom_label **Result:** Job will be labeled ``my_custom_label`` (no promolecular suffix for wavefunction files) ********************** Multiple Input Files ********************** NCIPLOT can analyze multiple molecules simultaneously: .. code:: bash chemsmart sub -s xz nciplot -f molecule1.xyz -f molecule2.xyz **Result:** Job label will be ``molecule1_and_molecule2`` **************************** Additional NCIPLOT Options **************************** CHEMSMART provides many options for customizing NCIPLOT calculations. For a complete list, use: .. code:: bash chemsmart sub nciplot --help Common options include: - ``-r, --rthres``: Distance threshold for grid extension - ``--ligand-file-number``: Specify ligand file for interaction analysis - ``--ligand-radius``: Radius of interaction from ligand - ``-i1, --intercut1``: Cutoff 1 for intermolecularity - ``-i2, --intercut2``: Cutoff 2 for intermolecularity - ``--fragments``: Define molecular fragments - ``--dgrid``: Use radial grids for promolecular densities - ``--integrate``: Trigger integration of properties - ``--grid-quality``: Set grid quality (coarse/fine/ultrafine) For more details on these options, refer to the original NCIPLOT program documentation and the command help.