Skip to content

Commands

Jump to bottom
Tony Schaefer edited this page May 19, 2021 · 11 revisions

Table of Contents

fuseRing

structure modification command that puts a ring on the selected atoms

usage

fuseRing atom selection rings ring names [newName residue names] [modify true | false]

fuseRing available

  • atom selection - selection of atoms
  • ring names - one or more (comma separated) ring names from the AaronTools ring library
  • residue names - change modified residue names to the specified names
  • modify - apply changes to the current structure or create a copy of the structure and modify that
  • available - print a list of available rings to the log

highlight

outline atoms and bonds to make them stand out more

usage

highlight selection [transparency 50] [color rgb(0,255,0)] [scale 1.5]

~highlight selection

  • transparency - transparency of highlight
  • color - color of highlight
  • scale - how much larger the highlights will be compared to their respective atoms or bonds

lookDown

reorient the molecule to align the vector from one atom to another along the x, y, or z axis

usage

lookDown atom1 [atom2 atom2] [axis x | y | z] [printRotation true | false]

  • axis - axis to which the vector is aligned; z is out of the plane of the screen
  • printRotation - print rotation matrix to the log

percentVolumeBuried

calculate volume buried by ligands around a metal center

%Vbur values are printed to the log. These values are useful for quantifying the steric bulk around a reaction center. See Organometallics 2008, 27, 12, 2679–2681 for more details.

usage

percentVolumeBuried model selection [radii UMN | Bondi] [scale 1.17] [method Lebedev | Monte-Carlo] [radialPoints 20 | 32 | 64 | 75 | 99 | 127] [angularPoints 110 | 194 | 302 | 590 | 974 | 1454 | 2030 | 2702 | 5810] [minimumIterations 25] [onlyAtoms atom selection] [centerAtoms atom selection] [radius 3.5]

  • radii - VDW radii for atoms
  • scale - scale VDW radii by this amount
  • method - numerical integration method
  • radialPoints - number of radial points for Lebedev integration
  • angularPoints - number of angular points for Lebedev integration
  • minimumIterations - minimum iterations for Monte-Carlo integration. Each iteration is a batch of 3000 points within the sphere. Iterations might continue beyond this if the integral has not converged.
  • onlyAtoms - only calculate the volume buried by the specified atoms. Default is all non-center atoms.
  • centerAtoms - uses specified atoms as the center. Default is any transition metal element.
  • radius - radius of sphere around center atom

pointGroup

Determine the point group (Schönflies) for a model

usage

pointGroup model selection [printElements true | false] [displayElements true | false] [tolerance 0.1] [axisTolerance 0.5] [maxRotation 6]

  • printElements - print symmetry elements (proper rotation axes, inversion centers, etc.) to the log
  • displayElements - add points, arrows, and discs to represent the inversion centers and axes or planes of symmetry
  • tolerance - tolerance for testing whether a symmetry element is valid
  • axisTolerance - tolerance in degrees for determining if two axes of symmetry are coincident
  • maxRotation - highest order proper rotations to test for

rmsdAlign

can be used to align structures to minimize the RMSD between them

RMSD values are printed to the log

usage

rmsdAlign model selection reference model selection [sort true | false] [align true | false]

  • sort - order the atoms based on a canonical ranking scheme before computing the RMSD
  • align - move structures to the reference. If false, the RMSD will be computed for the unmoved structure relative to the reference structure.

sterimol

calculate the L, B1, and B5 Sterimol parameters for substituents

parameter values are printed to the log

Sterimol parameters are useful for quantifying the size of an unsymmetric substituent. An overview of steric parameters can be found in Nature Chem 2012 4, 366–374.

usage

sterimol atom selection [radii UMN | Bondi] [showVectors true | false] [showRadii true | false]

  • atom selection - substituent(s)
  • radii - VDW radii to use
  • showVectors - display vectors for the Sterimol parameters. L: blue, B1:black, B5:red.
  • showRadii - display VDW radii as semi-transparent spheres around substituent atoms

substitute

change substituents on atomic structures

usage

substitute atom selection substituents substituent names [newName residue names] [guessAvoid true | false] [modify true | false] [useRemoteness true | false]

substitute available

  • atom selection - selection of atoms (the substituent atom bonded to the rest of the molecule or entire substituent)
  • substituent names - one or more (comma separated) substituent names from the AaronTools substituent library
  • residue names - change modified residue names to the specified names
  • guessAvoid - selected atom and the shortest group connected to it will be replaced with new substituents. Currently only looks within the selected atom's residue.
  • modify - apply changes to the current structure or create a copy of the structure and modify that
  • useRemoteness - attempt to use distance-based atom names, such as CA, CB, CG, etc.
  • available - print a list of available substituents to the log

tsbond

represent a bond as forming/breaking

all TS bonds for each model are grouped together, sharing color, radius, and transparency

usage

tsbond atom or bond selection [transparency 50] [color rgb(170,255,255)] [radius 0.16]

~tsbond atom or bond selection

  • transparency - transparency of bond group
  • color - color of bond
  • radius - width of bond
Clone this wiki locally