psico.orientation

Orientation, displacement and angle measurments of helices and domains.

3. 2010-2012 Thomas Holder, MPI for Developmental Biology

License: BSD-2-Clause

Functions

angle_between_domains(selection1, selection2)	Angle by which a molecular selection would be rotated when superposing on a selection2.
angle_between_helices(selection1, selection2)	Calculates the angle between two helices
cafit_orientation(selection[, state, ...])	Get the center and direction of a peptide by least squares linear fit on CA atoms.
func(selection1, selection2[, method, ...])	Angle by which a molecular selection would be rotated when superposing on a selection2.
helix_orientation(selection[, state, ...])	Get the center and direction of a helix as vectors.
loop_orientation(selection[, state, ...])	Get the center and approximate direction of a peptide.
plane_orientation(selection[, state, ...])	Fit plane (for example beta-sheet).
visualize_orientation(direction[, center, ...])	Draw an arrow.

psico.orientation.angle_between_domains(selection1, selection2, method='align', state1=-1, state2=-1, visualize=1, quiet=1, *, _self=...)

Angle by which a molecular selection would be rotated when superposing on a selection2.

Do not use for measuring angle between helices, since the alignment of the helices might involve a rotation around the helix axis, which will result in a larger angle compared to the angle between helix axes.

Usage

angle_between_domains selection1, selection2 [, method ]

Arguments

selection1 = string: atom selection of first domain

selection2 = string: atom selection of second domain

method = string: alignment command like “align” or “super” {default: align}

Example

fetch 3iplA 3iplB, async=0 select domain1, resi 1-391 select domain2, resi 392-475 align 3iplA and domain1, 3iplB and domain1 angle_between_domains 3iplA and domain2, 3iplB and domain2

See Also

align, super, angle_between_helices

psico.orientation.angle_between_helices(selection1, selection2, method='helix', state1=-1, state2=-1, visualize=1, quiet=1, *, _self=...)

Calculates the angle between two helices

Usage

angle_between_helices selection1, selection2 [, method [, visualize]]

Arguments

selection1 = string: atom selection of first helix

selection2 = string: atom selection of second helix

method = string: function to calculate orientation {default: helix_orientation}

visualize = 0 or 1: show fitted vector as arrow {default: 1}

Example

fetch 2x19, async=0 select hel1, /2x19//B/23-36/ select hel2, /2x19//B/40-54/ angle_between_helices hel1, hel2 angle_between_helices hel1, hel2, cafit

See Also

helix_orientation, loop_orientation, cafit_orientation, angle_between_domains

psico.orientation.cafit_orientation(selection, state=-1, visualize=1, guide=1, quiet=1, *, _self=...)

Get the center and direction of a peptide by least squares linear fit on CA atoms.

Usage

cafit_orientation selection [, visualize ]

Notes

Requires python module “numpy”.

See Also

helix_orientation

psico.orientation.func(selection1, selection2, method='align', state1=-1, state2=-1, visualize=1, quiet=1, *, _self=...)

Angle by which a molecular selection would be rotated when superposing on a selection2.

Do not use for measuring angle between helices, since the alignment of the helices might involve a rotation around the helix axis, which will result in a larger angle compared to the angle between helix axes.

Usage

angle_between_domains selection1, selection2 [, method ]

Arguments

selection1 = string: atom selection of first domain

selection2 = string: atom selection of second domain

method = string: alignment command like “align” or “super” {default: align}

Example

fetch 3iplA 3iplB, async=0 select domain1, resi 1-391 select domain2, resi 392-475 align 3iplA and domain1, 3iplB and domain1 angle_between_domains 3iplA and domain2, 3iplB and domain2

See Also

align, super, angle_between_helices

psico.orientation.helix_orientation(selection, state=-1, visualize=1, cutoff=3.5, quiet=1, *, _self=...)

Get the center and direction of a helix as vectors. Will only work for alpha helices and gives slightly different results than cafit_orientation. Averages direction of C(i)->O(i)->N(i+4).

Usage

helix_orientation selection [, visualize [, cutoff ]]

Arguments

selection = string: atom selection of helix

visualize = 0 or 1: show fitted vector as arrow {default: 1}

cutoff = float: maximal hydrogen bond distance {default: 3.5}

See Also

angle_between_helices, loop_orientation, cafit_orientation

psico.orientation.loop_orientation(selection, state=-1, visualize=1, quiet=1, *, _self=...)

Get the center and approximate direction of a peptide. Works for any secondary structure. Averages direction of N(i)->C(i) pseudo bonds.

Usage

loop_orientation selection [, visualize ]

See Also

helix_orientation

psico.orientation.plane_orientation(selection, state=-1, visualize=1, guide=0, quiet=1, *, _self=...)

Fit plane (for example beta-sheet). Can also be used with angle_between_helices (even though this does not fit helices).

Returns center and normal vector of plane.

psico.orientation.visualize_orientation(direction, center=[0.0, 0.0, 0.0], scale=1.0, symmetric=False, color='green', color2='red', *, _self=...)

Draw an arrow. Helper function for “helix_orientation” etc.