ASL Aliases
Maestro allows you to define your own aliases, using either the Command Input Area or the Preferences Panel, under Shortcuts. Maestro converts all aliases into their corresponding commands before performing operations involving the aliased commands. You must ensure that aliases produce sensible results. Some aliases are supplied with the distribution. These are defined in the file mmasl.ini, which is in the mmshare-v7.3/data directory. For reference, they are listed in the table below.
The alias "ligand" is a special alias that is dynamically defined by settings made in the Ligand Detection Preferences of the Preferences Panel. The expression is constructed from conditions on the minimum and maxmum number of heavy (non-hydrogen) atoms, the presence or absence of specified residues in the ligand, whether to include ions, and whether to include molecules that contain only amino acids.
| Aliases | ASL Expression |
|---|---|
| intersection, INTERSECTION, & | and |
| UNION, union, | | or |
| ! | not |
| MOL, mol | mol. |
| ATOM, atom | atom. |
| RES, res | res. |
| CHAIN, chain | chain. |
| backbone, BACKBONE | ((res.pt ACE) OR (atom.pt ca,c,n,o,oxt OR (a.e H and withinbonds 1 atom.pt ca, n)) and not (res.pt hoh or res.pt spc or res.pt t4p or res.pt t3p or res.pt t5p or res.pt t4pe or res.pt t4pd or res.pt spce or res.pt t4p5 or res.pt DPPC, POPC, POPE, DMPC, DOPC, DOPS, POPS, DPPS, DMPS, DPPE, DMPE, DOPE, PIP, POPA, DOPA, DMPA, DPPA or (res.pt GLY AND atom.pt 2HA, HA3))) |
| SIDECHAIN, sidechain | ((atom.pt 3HE, 1HG, OD1, OD2, HB, HE, HG, HH, 3HD1, 3HD2, 2HG1, 1HZ, 2HG2, HZ2, HZ3, 3HZ, CE1, CE2, CE3, HG1, HZ, OE1, OE2, 2HD1, 2HD2, 1HG1, 1HG2, 2HH1, 2HH2, 2HB, HD1, HD2, 2HD, 2HE, 2HG, HH2, ND1, ND2, NH1, NH2, 1HD1, CZ2, CZ3, 2HE2, 1HH1, NE, 1HH2, 2HZ, CG1, CG2, HE1, HE2, HE3, NE1, CB, NE2, OG1, CD, CE, NZ, CG, 1HE2, 3HG1, 3HG2, OG, OH, SD, CD1, CD2, SG, 1HB, CH2, 1HD, 3HB, CZ, 1HE, 1HD2, HH1, HE3, HD13, HD23, HG12, HZ1, HG21, HD12, HD22, HG11, HH12, HH22, HB2, HG2, HD11, HE22, HH11, HH21, HE21, HG13, HG23, HB3, HD21, HG3, HB1, HG22, HD3 ) or ( res.pt MSE & atom.pt "SE ") or ( res.pt gly & atom.pt 2ha,ha3 ) and not (res.pt gly & atom.pt 1ha,ha2 ) and not ( res.pt DPPC, POPC, POPE, DMPC, DOPC, DOPS, POPS, DPPS, DMPS, DPPE, DMPE, DOPE, PIP, POPA, DOPA, DMPA, DPPA) ) |
| WATER, water | (/H2-O3-H2/ or atom.mtype OW or res.pt hoh, spc, t4p, t3p, t5p, t4pe, t4pd, spce, t4p5, dod) |
| SOLVENT, solvent | (/H2-O3-H2/ or atom.mtype OW or res.pt hoh, spc, t4p, t3p, t5p, t4pe, t4pd, spce, t4p5, dod or res.pt GOL, EDO, DMS, PEG, MPD, PG4, BME, PGE, IPA, 1PE, EOH, P6G, DMF, MOH, POL, 2PE, PE4, ETA, 15P, 12P, P33, PE5, TBU, CCN, CXE, 7PE, NME, PE3, PE6, ACN, P4C, PE8, NEH, XPE, 1BO, N8E, DMN, CE1, PYE, C10, SBT, MB3) |
| IONS, ions | (fillmol ( atom.formalcharge <0 or atom.formalcharge > 0 ) and (mol.atoms < 10 ) ) |
| MEMBRANE, membrane | ( res. POP, POPE, POPC, DPPC, DMPC ) |
| protein, PROTEIN | (fillres at.pt " CA " or res.pt ACE) |
| workspace_selection | atom.selected |
| displayed_atoms, DISPLAYED_ATOMS | atom.disp |
| protein_near_ligand, PROTEIN_NEAR_LIGAND | fillres( (fillres at.pt " CA " or res.pt ACE) and within 5.0 ligand ) |
| all_hydrogens, ALL_HYDROGENS | atom.ele H |
| non_polar_hydrogens, NON_POLAR_HYDROGENS | (atom.ele H and /C0-H0/) |
| non_polar_ligand_hydrogens, NON_POLAR_LIGAND_HYDROGENS | (atom.ele H and /C0-H0/ and ligand) |
| polar_hydrogens, POLAR_HYDROGENS | (atom.ele H and not /C0-H0/) |
| heavy_atoms, HEAVY_ATOMS | not atom.ele H |
| METALLOIDS, metalloids | atom.atomicnum 5,14,32,33,51,52,84,85 |
| METALS, metals | atom.atomicnum 3,4,11-13,19-31,37-50,55-83,87-109 |
| NUCLEIC_ACIDS, nucleic_acids | (res. " DA "," DC "," DG "," DT "," C "," U "," G "," A ") |
| receptor, RECEPTOR | ( ( (fillres at.pt " CA " or res.pt ACE) or (res. " DA "," DC "," DG "," DT "," C "," U "," G "," A ") ) and ( not ligand )) |
| DNA, dna | (res. " DA "," DC "," DG "," DT ") |
| RNA, rna | (res. " C "," U "," G "," A ") |
| NUCLEIC_BACKBONE, nucleic_backbone | (res. " DA " " DC " " DG " " DT " " C " " U " " G " " A " AND NOT atom.pt N9 N1 AND withinbonds 1 atom.pt " C3'" " O3'" " O5'" P " C4'" " C5'" " O4'" " C1'" " C2'" " O2'") |
| NUCLEIC_SIDECHAIN, nucleic_sidechain | (res. " DA " " DC " " DG " " DT " " C " " U " " G " " A " AND NOT atom.pt " C1'" AND withinbonds 1 atom.pt N1 C2 N2 O2 N3 C4 N4 O4 C5 C6 N6 O6 C7 N7 C8 N9) |