NCIPLOT Tutorial

This section will cover NCIPLOT analysis capabilities in CHEMSMART.

Note

For NCI visualization using PyMOL, see Interaction Analysis (PyMOL).

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 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)

                            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

Promolecular Density

Wavefunction Density

Usage Examples

Example 1: Using XYZ File (Promolecular Density)

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)

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)

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:

# 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)

# 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:

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:

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.