names and keywords can be abbreviated to non-ambiguous prefixesīest practice recommendation: Only write case-sensitive, non-abbreviated selection expressions.names and keywords are case-insensitive unless ignore_case is set.The following table lists the details how they differ. There are serveral very similar operators that select by pairwise atom distances. Same as within, but excludes S2 from the selection (and thus is identical to S1 and S2 around 12.3)Ītoms in S1 that are at least 12.3 Anstroms away from S2Ītoms with model-space z coordinate greater than 12.3Īuto-assigned in Incentive PyMOL 1.4-1.8) Proximity (see also comparison of distance operators)Ītoms in S1 that are within 12.3 Angstroms of any atom in S2Ītoms with centers within 12.3 Angstroms of the center of any atom in S1Įxpands S1 by atoms within 12.3 Angstroms of the center of any atom in S1Ītoms whose VDW radii are separated from the VDW radii of S1 by a minimum of 1.2 Angstroms. Important: All "by"-operators have a weak priority, so (byres S1 or S2) is actually identical to (byres (S1 or S2)) and not to ((byres S1) or S2)ĬA atoms of residues with at least one atom in S1Įxpands S1 to complete molecules (connected with bonds)Īll rings of size ≤ 7 which have at least one atom in S1 (new in PyMOL 1.8.2)Ītoms directly bonded to S1, may include S1Įxpands S1 by 3 bonds connected to atoms in S1
AUTO ASSIGN CARBONS MESTRENOVA CODE
Protein residue sequence with one-letter code "ACDEF" (see also FindSeq)Ītoms with label "Hello World" (new in PyMOL 1.9)Ītoms in S1 whose identifiers name, resi, resn, chain and segi all match atoms in S2Ītoms in S1 whose identifiers name and resi match atoms in S2 Per-object atom index at load time (see also retain_order) Internal per-object atom index (changes with sorting) Segment identifier "S" ( label_asym_id from mmCIF) Named selection or object "sele", or empty selection if "sele" doesn't exist Named selection or object "sele" Recommended, avoids ambiguity Named selection or object "sele", but only if it doesn't conflict with the name of another operator The dummy variables s1 and s2 stand for selection-expressions such as "chain a" or "hydro." Selection operators and modifiers are listed below.