/object-name/segi-identifier/chain-identifier/resi-identifier/name-identifier
commonly:
///chain-identifier/resi-identifier/name-identifierExamples:
///A/125/CA |
///D/58/NZ |
| Single Word
Selector | Short Form | Description |
|---|---|---|
| all | * | All atoms currently loaded into PyMOL |
| none | none | No atoms (empty selection) |
| hydro | h. | All hydrogen atoms currently loaded into PyMOL |
| hetatm | het | All atoms loaded from Protein Data Bank HETATM records |
| visible | v. | All atoms in enabled objects with at least one visible representation |
| present | pr. | All
atoms with defined coordinates in the current state
(used in creating movies) |
| Matching
Property Selector | Short Form | Description | Identifier - List of | Example |
|---|---|---|---|---|
| symbol | e. | atomic symbols | 1- or 2-letter chemical symbols from the periodic table | select PolarFe, symbol o+n+Fe |
| name | n. | PDB Atom Names | up to 4-letter codes for atoms in proteins or nucleic acids | select carbons, name ca+cb+cg+cd |
| resn | r. | Residue Names | 3-letter codes for amino acids | select aas, resn asp+glu+asn+gln
orup to 2-letter codes for nucleic acids
select bases, resn a+g |
| resi | i. | Residue number | up to 4-digit residue numbers | select mults10, resi 1+10+100+1000
select nterm, resi 1-10 |
| chain | c. | PDB Chain ID | single letters or sometimes numbers | select firstch, chain a |
| segi | s. | Segment ID | up to 4 letter identifiers | select ligand, segi lig |
| ss | ss | secondary structure | single letters | select allstrs, ss h+s+l+"" |
Other property selectors - select by comparison to numeric identifiers:
| Numeric
Selector | Short Form | Description | Argument | Example |
|---|---|---|---|---|
| b | b | b-factor-value | real number | select fuzzy, b > 10 |
| q | q | occupancy-value | real number | select lowcharges, q <0.50 |
| formal_charge | fc. | formal charge-value | integer | select doubles, fc. = -1 |
| partial_charge | pc. | partial charge-value | real number | select hicharges, pc. > 1 |
| hide representation
show representation |
e.g. hide sticks, show cartoon, etc |
| zoom selection-expression | zooms display to focus on selection |
| color specific-color, selection-expression | e.g. color red, mysubunit2 |
| png file-name | save current view as a PNG graphic |