![]() Aligning trajectories based on an atom selection and calculate RMSF of alpha carbons NAMD 2.x is also required for energy interaction calculations. Prior to running these commands, CHARMM-GUI for system preparation and NAMD 3.0 alpha was used for running the simulations, therefore the codes should be adapted for other production outputs. This page lists several commands and mini-tutorials useful for bioinformatics purposes in protein simulations analyses using VMD (v. align_button.tcl – a script replicating the function of the ALIGN button from the RMSD Visualizer Tool ( with regards to Bassam Haddad).rmsf.tcl – a script for calculating RMSF over an atom selection, I got this over the internet, but could not track its original source.In radians, accounting for periodic boundary conditions. dihedral(i, j, k, m): gives the dihedral angle between atoms i, j, k and m.angle(i, j, k): gives the angle between atoms i, j and k in radians,Īccounting for periodic boundary conditions.distance(i, j): gives the distance in Ångströms between atoms i and j,Īccounting for periodic boundary conditions.This will return 0 if the property is not set īut some properties apply to multiple atoms, and as such are only usable when : gives the value of the numeric property named ‘property’įor the atom.resid: gives the atomic residue index.vx, vy and vz: gives the atomic velocity in cartesian coordinates.x, y and z: gives the atomic position in cartesian coordinates.index: gives the atomic index in the frame.Most of the numeric properties only apply to a single atom: Is_angle(type C, #1, name O) select all atoms in the midle of a C-X-O angle. Is_bonded(#1, name O) select all atoms bonded to an oxygen and In the latter case, all the atoms in the sub-selectionĪre checked to see if any of them verify the selection. This will return false if the propertyįor boolean selectors taking arguments, i/j/k/m can either be one of theĪtoms currently being matched ( #1 / #2 / #3 / #4) or another selection : check if atoms have a boolean property named ‘property’.IfĪny of i, j, k or m refer to the same atom, this returns false is_improper(i, j, k, m): check if atoms i, j, k and m are bonded together.If any of i, j, k or m refer to the same atom, this returns that i is bonded to j, j is bonded to k, and is_dihedral(i, j, k, m): check if atoms i, j, k and m are bonded together.K refer to the same atom, this returns false that i is bonded to j and j is bonded to k. is_angle(i, j, k): check if atoms i, j and k are bonded together to formĪn angle, i.e.Refers to the same atom, this returns false is_bonded(i, j): check if atoms i and j are bonded together.none: never matches an atom and returns false.all: always matches any atom and returns true.name(#1) = H and not x(#1) < 5.0 and (z(#2) < 45 and name(#4) = O) or name(#1) = C are complex selections using booleans Is true if both side of the expression are true the or operator is true ifĮither side of the expression is true and the not operator reverse true toįalse and false to true. Will give the name of the third atom, and so on.įinally, constraints are combined with boolean operators. When using a selection with more than one atom, selectors must refer to theĭifferent atoms with #1, #2, #3 or #4 variables: name(#3) These operations follow the usual priority rules: Supported, as well as ^ for exponentiation and % for modulo (remainder Mathematical operations: the usual +, -, * and / operators are Numeric values are produced by numeric selectors ( x mass, …) or angles: name(#2) = O and mass(#3) (more than), and >= (more or For example, atoms: name = H will select all atoms whose name is One, two, three or four independent atoms and bonds, angles andĭihedrals for two, three or four bonded atoms.Ī selection is built using a context and a set of constraints separated by aĬolon. Existing contextes areĪtoms or one, pairs or two, three and four to select Selecting, and the relation between these atoms. That they are multiple selections: we can select more than one atom at once.Īll selections starts with a context, indicating the number of atoms we are For examples, atom: name H and x > 15 would select all single atoms whose name is H and xĬhemfiles selections differs from the well-known VMD selections by the fact Chemfiles selection language allows to select some atoms in a Frame matching a set of constraints.
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