psico.xtal

Crystallographic symmetry related commands.

3. 2010-2012 Thomas Holder

License: BSD-2-Clause

Functions

biomolecule([name, filename, prefix, ...])	Create biological unit (quaternary structure) as annotated by the REMARK 350 BIOMOLECULE record.
cell_axes([object, a_color, b_color, ...])	Draw arrows corresponding to the crystallographic axes.
cellbasis(angles, edges)	API only.
pdbremarks(filename, *[, _self])	API only.
supercell([a, b, c, object, color, name, ...])	Draw a supercell, as requested by Nicolas Bock on the pymol-users mailing list (Subject: [PyMOL] feature request: supercell construction Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
symexpcell([prefix, object, a, b, c, _self])	Creates all symmetry-related objects for the specified object that occur with their bounding box center within the unit cell.

Classes

PutCenterCallback(name[, corner])

class psico.xtal.PutCenterCallback(name, corner=0)

Bases: object

load()

prev_v = None

psico.xtal.biomolecule(name=None, filename=None, prefix=None, number=1, suffix=None, quiet=0, *, _self=...)

Create biological unit (quaternary structure) as annotated by the REMARK 350 BIOMOLECULE record.

Usage

biomolecule name [, filename [, prefix [, number ]]]

Arguments

name = string: name of object and basename of PDB file, if filename is not given {default: first loaded object}

filename = string: file to read remarks from {default: <name>.pdb}

prefix = string: prefix for new objects {default: <name>}

Example

fetch 1rmv, async=0 biomolecule 1rmv

psico.xtal.cell_axes(object=None, a_color='0xd95f02', b_color='0x1b9e77', c_color='0x7570b3', name='cell_axes')

Draw arrows corresponding to the crystallographic axes.

The default color palette is colorblind friendly but close to the familiar red, green, and blue for the a, b, and, c axes respectively. (See https://colorbrewer2.org/#type=qualitative&scheme=Dark2&n=3 for details)

Usage

cell_axes [ object, [, a_color [, b_color [, c_color, [ name]]]]

Arguments

object = string: name of object to take cell definition from

a_color = string: color of a-axis {default: ‘0xd95f02’}

b_color = string: color of b-axis {default: ‘0x1b9e77’}

c_color = string: color of c-axis {default: ‘0x7570b3’}

name = string: name of the cgo object to create {default: cell_axes}

psico.xtal.cellbasis(angles, edges)

API only. For the unit cell with given angles and edge lengths calculate the basis transformation (vectors) as a 4x4 numpy.array

psico.xtal.pdbremarks(filename, *, _self=...)

API only. Read REMARK lines from PDB file. Return dictionary with remarkNum as key and list of lines as value.

psico.xtal.supercell(a=1, b=1, c=1, object=None, color='green', name='supercell', withmates=1, prefix='m', *, _self=...)

Draw a supercell, as requested by Nicolas Bock on the pymol-users mailing list (Subject: [PyMOL] feature request: supercell construction Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))

Usage

supercell a, b, c [, object [, color [, name [, withmates [, prefix]]]]]

Arguments

a, b, c = integer: repeat cell in x,y,z direction a,b,c times {default: 1,1,1}

object = string: name of object to take cell definition from

color = string: color of cell {default: blue}

name = string: name of the cgo object to create {default: supercell}

withmates = bool: also create symmetry mates in displayed cells {default: 1}

prefix = string: prefix for names of symmetry mates {default: m}

See Also

show cell

psico.xtal.symexpcell(prefix='mate', object=None, a=0, b=0, c=0, *, _self=...)

Creates all symmetry-related objects for the specified object that occur with their bounding box center within the unit cell.

Usage

symexpcell prefix, object, [a, b, c]

Arguments

prefix = string: prefix of new objects

object = string: object for which to create symmetry mates

a, b, c = integer: create neighboring cell {default: 0,0,0}

See Also

symexp