Geometry (COG) of a given selection, e.g. Selects all atoms within a cylindric zone centered in the center of cyzone externalRadius zMax zMin selection Radius 2.4 and external radius 6.0 around the COG. Protein, resid 130, resid 80 and creates a spherical layer of inner Geometry (COG) of a given selection, e.g., sphlayer 2.4 6.0 ( protein and ( resid 130 or resid 80 ) ) selects the center of geometry of Selects all atoms within a spherical layer centered in the center of sphlayer innerRadius externalRadius selection Resid 130, resid 80 and creates a sphere of radius 6.0 around the COG. sphzone 6.0 ( protein and ( resid 130 or resid 80 ) ) selects the center of geometry of protein, Selects all atoms within a spherical zone centered in the center of ![]() That are within 3.5 Angstroms from the protein sphzone externalRadius selection around 3.5 protein selects all atoms not belonging to protein Selects all atoms a certain cutoff away from another selection,Į.g. select_atoms ( "around 6 protein", periodic = False ) Out: around distance selection This can be turned off by passing in the keyword periodic=False: The geometric keywords below all implement periodic boundary conditions by default when valid cell dimensions are accessible from the Universe. protein and not (resname ALA or resname LYS) selects all atoms that belong to a protein, but are not in a lysine or alanine residue Geometric protein and not resname ALA selects all atoms that belong to a protein but are not in an alanine residue or Boolean notĪll atoms not in the selection, e.g. At the moment, only the TPR format defines the moltype. Select by the moltype topology attribute, e.g. icode selects atoms without insertion codes. With residue numbers using the resid selector above.Į.g. icode icodeĪ selector for atoms where insertion codes are available. resid 4 and resname ALA and altloc B selects only the atoms of ALA-4 Often the case with high-resolution crystal structuresĮ.g. DMPC 1 C2 selects the C2 carbon of the first residue of theĪ selection for atoms where alternative locations are available, which is atom seg-name residue-number atom-nameĪ selector for a single atom consisting of segid resid atomname,Į.g. This uses the Atom.type topology attribute. the CHARMM PSFįile contains numeric atom types). The force field it is read from the topology file (e.g. Select by atom type this is either a string or a number and depends on Example: name CA (for C-alpha atoms) or name OW (for SPC water oxygen) type atom-type Select by atom name (as given in the topology). Unlike resid, resnum is insensitive to insertion codes. A residue number (“resnum”) is taken directly from the A rangeĬonsists of two numbers separated by a colon (inclusive) suchĪs resnum 1:5. Resnum can take a single residue number or a range of numbers. Unlike resnum, resid is sensitive to insertion codes. This selects all residues with resid=1Ī residue number (“resid”) and icode is taken directly from the A range consists of two selections separated by a colon Resid can take a single residue number or a range of numbers, followedīy insertion codes. Select by segid (as given in the topology), e.g. ![]() These have the names: C1’, C2’, C3’, C4’, O2’, O4’, O3’ segid seg-name These atoms have the names: P, O5’, C5’, C3’, O3’ nucleicbase Selects the backbone atoms of a hard-coded set of nucleic residues. Selects atoms that belong to a hard-coded set of standard nucleic residue names. Selects the backbone atoms of a hard-coded set of protein residues. Selects atoms that belong to a hard-coded set of standard protein residue names. Any number of patterns can be included in the search.įor more information on pattern matching, see the fnmatch documentation. The string GL* selects all strings that start with “GL”, Using * in a string matches any number of any characters select_atoms() also accepts keywords that modify the behaviour of the selection string and the resulting AtomGroup (documented further down this page). This page documents selection keywords and their arguments. When order matters, you can pass in multiple phrases. Which can happen with complicated selections. This is to ensure that there are not any duplicates, A single selection phrase always returns anĪtomGroup with atoms sorted according to their ![]() These two methods have different behaviour: while lect_atoms operates on all the atoms in the universe, lect_atoms only operates on the atoms within the original AtomGroup. select_atoms ( 'resname ALA' ) In : ala Out: ĪtomGroup. In : import MDAnalysis as mda In : from import PSF, DCD In : u = mda. Standard residues in MDAnalysis selections.
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