Basic Visualization (PyMOL)

This page covers molecular visualization capabilities using PyMOL for creating high-quality graphics and interactive session files.

Visualization Jobs

Create static PyMOL visualizations and interactive PSE session files.

chemsmart run [OPTIONS] mol [MOL_OPTIONS] visualize [SUBCMD_OPTIONS]

Visualization Options

Option	Type	Description
`-f, --file`	string	PyMOL style script (default: zhang_group_pymol_style.py)
`-s, --style`	string	Render style (see Visualization Styles)
`-t, --trace/--no-trace`	bool	Ray trace rendering (default: enabled)
`-v, --vdw`	bool	Add Van der Waals surface (default: disabled)
`-q, --quiet/--no-quiet`	bool	Quiet mode (default: disabled)
`--command-line-only/--no-command-line-only`	bool	Run without GUI (default: enabled)
`-c, --coordinates`	string	Coordinates for labeling (1-indexed)

Basic Usage

Standard visualization:

chemsmart run mol -f molecule.xyz visualize

Quiet mode:

chemsmart run mol -f calculation.log visualize -q

With coordinate labeling:

chemsmart run mol -f structure.xyz visualize -c [[1,2,3]]

Custom style:

chemsmart run mol -f molecule.log visualize -f custom_style.py

Batch visualization from a directory (by file type):

chemsmart run mol -d /path/to/outputs -t log visualize

This creates a single PyMOL session visualizing the last structure of every .log file in the directory.

Batch visualization from a directory (by program):

chemsmart run mol -d /path/to/outputs -p gaussian visualize

This creates a single PyMOL session visualizing the last structure of all Gaussian output files in the directory.

Movie Jobs

Generate rotating movie animations.

chemsmart run [OPTIONS] mol [MOL_OPTIONS] movie [SUBCMD_OPTIONS]

Movie jobs inherit all visualization options.

Basic Usage

chemsmart run mol -f molecule.xyz movie

Hybrid Visualization

Create visualizations with different groups displayed in different styles.

chemsmart run [OPTIONS] mol [MOL_OPTIONS] visualize --hybrid [SUBCMD_OPTIONS]

Hybrid Options

Option	Type	Description
`-H, --hybrid`	bool	Enable hybrid visualization mode
`-G, --group`	string	Atom indices for a group (repeatable)
`-C, --color`	string	Color for each group (repeatable)
`-SC, --surface-color`	string	Surface color (default: grey)
`-ST, --surface-transparency`	string	Surface transparency (default: 0.7)
`-NC, --new-color-carbon`	string	Carbon atom color (RGB list)
`-NN, --new-color-nitrogen`	string	Nitrogen atom color (RGB list)
`-NO, --new-color-oxygen`	string	Oxygen atom color (RGB list)

Basic Usage

Basic hybrid visualization:

chemsmart run mol -f molecule.xyz visualize --hybrid -G '1,2,3'

Custom colors:

chemsmart run mol -f molecule.log visualize --hybrid -G '1,2,3' -G '4,5,6' -C cbay -C cbak

Custom background settings:

chemsmart run mol -f structure.xyz visualize --hybrid -G '1,2,3' -ST 0.8 -NC '[0.8, 0.8, 0.9]'

Example

chemsmart run mol -f molecule.xyz visualize --hybrid -G '417-418,422-424' -G '336,397-412'

Visualization Styles

Use -s/--style on the visualize subcommand to select a render style. Base styles use zhang_group_pymol_style.py; scientific styles use zhang_group_scientific_styles.py and are routed through PyMOLScientificStyleVisualizationJob.

`-s` value	Template	Description
`pymol`	`zhang_group_pymol_style.py`	Default PyMOL ball-and-stick visualization
`cylview`	`zhang_group_pymol_style.py`	Cylindrical stick representation
`glossy`	`zhang_group_scientific_styles.py`	Glossy semi-metallic rendering with transparent PNG export
`comic`	`zhang_group_scientific_styles.py`	Comic ball-and-stick rendering with black outlines and element labels
`soft-cartoon`	`zhang_group_scientific_styles.py`	Soft pastel ball-and-stick with radius-ratio coordination spheres and illustrated outlines
`editorial-minimal`	`zhang_group_scientific_styles.py`	Matte minimal ball-and-stick style for main-text mechanistic figures
`soft-ceramic`	`zhang_group_scientific_styles.py`	Soft ceramic / studio ball-and-stick style for coordination complexes
`neon-coordination-core`	`zhang_group_scientific_styles.py`	Neon coordination-core emphasis using radius-ratio shells and a transparent background
`matte-clay`	`zhang_group_scientific_styles.py`	Matte clay ball-and-stick using radius-ratio coordination spheres and core hydrogens
`xray-wire`	`zhang_group_scientific_styles.py`	Monochrome wireframe style for SI structure verification
`steric-surface`	`zhang_group_scientific_styles.py`	Transparent molecular surface for steric / space-filling views
`quasi-chemdraw-bold`	`zhang_group_scientific_styles.py`	Bold ChemDraw-like style using radius-ratio cores and flat illustrative shading

Basic Usage

Standard PyMOL style:

chemsmart run mol -f molecule.xyz visualize
chemsmart run mol -f molecule.xyz visualize -s pymol
chemsmart run mol -f molecule.xyz visualize -s cylview

Scientific styles:

chemsmart run mol -f complex.xyz visualize -s glossy
chemsmart run mol -f complex.xyz visualize -s comic
chemsmart run mol -f complex.xyz visualize -s soft-cartoon
chemsmart run mol -f complex.xyz visualize -s editorial-minimal

Highlight metal–ligand bonds with -c. In comic style, each pair is drawn as a ball-and-stick bond; numeric distance labels are hidden so element labels remain visible. Other scientific styles keep the usual dashed distance measurements.

chemsmart run mol -f complex.xyz visualize -s comic \\
    -c '[[1,2],[1,5],[1,36],[1,3],[1,15],[1,8]]'

Note

-H/--hybrid and derived -s styles are mutually exclusive. Scientific styles resolve the metal center and coordinating atoms via the radius-ratio select_coordination algorithm. Ray-traced PNG export uses a transparent background for compositing.

Examples

Glossy

Comic

Soft cartoon

Editorial minimal

Soft ceramic

Neon coordination core

Matte clay

X-ray wire

Steric surface

Quasi-ChemDraw bold

Align Jobs

Align multiple molecular structures for comparison (Alignment reference is the first structure).

chemsmart run [OPTIONS] mol align [SUBCMD_OPTIONS]

Basic Usage

Align multiple files:

chemsmart run mol -f mol1.xyz -f mol2.gjf -f mol3.log -i 1 align

Align all files of the same type:

chemsmart run mol -d . -t xyz -l xyz_alignment align

Note

When using -i n, ensure every input file contains the nth structure. Here -t/--filetype is extension-based: it filters filenames such as .xyz or .log and does not infer a Gaussian or ORCA program identity.

Align multiple structures in one file:

chemsmart run mol -f conformers.xyz -i 1,3-6,-1 align

Note

If there is no additional index, align all structures in the file by default.