Selecting atoms¶

The browser and VS Code command bar has two modes. AtomWorks query selects atoms in either renderer, using expressions or sel() for selection paths. PyMOL commands selects and styles atoms through Patinae.

Picking in the viewer¶

The Pick control is always visible in the viewer toolbar:

Atoms (default): clicking a cartoon only reveals local sticks and focuses the view. Click atoms in those sticks to add or remove individual atoms.
Residues: clicks toggle the whole residue, including clicks on sticks.
Chains: clicks toggle the whole chain.

A click adds all targeted atoms if any are unselected, or removes them if all are selected. Atoms outside that target never change. There is no automatic refinement based on previous clicks and no modifier key is required. In Atoms mode, selecting one atom within an already selected residue removes only that atom.

Showing local sticks and moving the camera do not change selection. Clear selection empties the selection while leaving local sticks available. Query and sequence-range selections explicitly replace the selection; pending canvas requests are cancelled by Clear, replacement selections, picking-mode changes, or document changes.

Clicking a residue in the sequence toggles that whole residue without changing other selected atoms. Clicking a partially selected residue selects the rest of it; clicking again removes it. Enter and Space behave the same way.

The sequence strip fills fully selected residues and partially fills residues with only some atoms selected. All selection counts share the same editing state.

All actions use this same selection: condition edits, charges, bonds, deletion, measurements, and selection styling. The Pick control determines what future viewer clicks select; changing it or the condition type leaves existing selections unchanged. Conditions that inherently operate on residues or chains apply to the whole residues or chains containing selected atoms, using the same shared editing logic as the native PyMOL plugin. The condition editor explains this expansion.

AtomWorks query¶

Queries are expressions over the current structure’s annotations. Studio uses AtomWorks’ QueryExpression; this field is not a Python console.

Expression	Selects
`atom_name == 'CA'`	Alpha carbons.
`chain_id == 'A' and res_id >= 10 and res_id <= 20`	Residues 10–20 in chain A.
`element in ['N', 'O']`	Nitrogen and oxygen atoms.
`atom_name not in ['N', 'CA', 'C', 'O']`	Atoms outside those four names.
`has_bonds()`	Atoms participating in stored bonds.
`has_nan_coord()`	Atoms with missing coordinates.
`sel('[A,B]///CA')`	A path selection inside an expression.

Use and, or, and not, or parenthesized comparisons with &, |, and ~. Names must be stored annotations, supported query functions, or annotations that AtomWorks can derive. Derived fields are evaluated on a temporary copy; selecting atoms does not change the saved document or undo history.

chain_id is the source chain identifier. Assembly copies can share it. chain_iid identifies the chain instance shown in Studio; for example, chain_iid == 'A_1' selects that instance if it exists. Inspect your structure before assuming either identifier. res_id is a residue number, not its position in the displayed sequence; atom_id is an annotation, not a zero-based row index.

Selection paths¶

Use sel('A/*/[10-20]/CA') in AtomWorks query to select alpha carbons in residues 10–20 of chain A. A path describes atoms, not a filesystem location. You can combine it with expressions, for example sel('A') and element == 'N'.

Wrap the paths below in sel('...'). Fields appear in this order:

CHAIN_ID / RES_NAME / RES_ID / ATOM_NAME / TRANSFORMATION_ID

Use * for any value. Omitted trailing fields are wildcards. Lists and residue ranges go inside brackets; top-level commas join selections.

Path	Selects
`A`	Source chain A, including its assembly copies.
`*/ALA`	All alanine residues.
`//*/CA`	Alpha carbons.
`[A,B]///[N,CA,C,O]`	Those backbone atoms in chains A and B.
`A/*/[10-20,25]`	Residues 10–20 and 25 in A.
`A//[10-20], B//[3-8]`	Two different residue ranges.
`A///CA/1`	Alpha carbons in transformation 1 of A.

Ranges are inclusive. Write [10-20], not bare 10-20. Studio delegates parsing to AtomWorks’ AtomSelectionStack; it does not maintain a separate grammar. A valid query with no matching atoms selects zero atoms. In a union, an unmatched member does not discard the matching members.

PyMOL commands¶

With Patinae active, select PyMOL commands and try:

select sele, name CA
show spheres, sele

The select command also updates Studio’s editing selection, so an annotation applies to those atoms. deselect clears it. Invalid commands retain the input and selection for correction. More contains the supported command list. Only Patinae’s supported PyMOL-style commands work here; arbitrary PyMOL commands, aw_* plugin commands and Python are not supported. remove <selection> uses Studio’s delete operation, updating the annotated CIF and the viewer together. Undo restores the atoms and their annotations. For example, remove solvent removes water when present. Other structural commands such as alter and bond remain disabled; use Studio’s editing controls. Mol* uses AtomWorks query and its menus instead.

Inside the native PyMOL application, use the normal PyMOL selection language:

select sele, name CA
show spheres, sele

Then apply edits through the Studio panel. PyMOL uses its own selection parser; AtomWorks expressions such as atom_name == 'CA' belong in the browser’s AtomWorks query mode. See the PyMOL guide for console commands and the distinction between the displayed molecule and the saved document.

Show and hide atoms¶

Style uses the same controls in Studio, VS Code, and embedded Gradio. Choose All atoms or Selection, then Show, Hide, or Show only and a representation. Show only replaces other representations on that target. Hide everything hides all representations on the target; it does not delete atoms.

For a binding-site view, select the protein and show a cartoon, then select the ligand and show sticks. Show a surface to inspect the pocket and hide that surface when it obscures contacts. Both Patinae and Mol* support these controls. Ribbon uses Mol*’s backbone representation; rendering details differ between engines.

Display changes leave the annotated CIF and edit history unchanged. Selection styles stay attached to the selected atoms through annotation refreshes and renderer switches. Opening another structure or changing its atom inventory resets these styles. Structural changes still go through AtomWorks and Undo.