Get raw distances

Type	Python Module
Download	get_raw_distances.py
Author(s)	Takanori Nakane and Thomas Holder
License	BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	psico.querying

get_raw_distances can dump distance objects, created with distance.

This script also provides the command select_distances, which selects atoms from distance objects.

Warning: the atoms are hashed by coordinates; this could cause issues if coordinates are altered after distance objects have been created (see also dynamic_measures setting).

Usage

get_raw_distances [ names [, state [, selection ]]]

select_distances [ names [, name [, state [, selection [, cutoff ]]]]]

Arguments

• names = string: names of distance objects (no wildcards!) {default: all measurement objects}
• state = integer: object state {default: 1}
• selection = string: atom selection {default: all}

Example

fetch 2xwu, async=0

# interface polar contacts
distance iface_hbonds, chain A, chain B, mode=2

# dump (model,index) information
get_raw_distances iface_hbonds

Example Atom Selection

# select atoms
select_distances iface_hbonds, hbsele

# nice representation
set cartoon_side_chain_helper
set sphere_scale, 0.5
as cartoon, 2xwu
show sticks, byres hbsele
show spheres, hbsele

See Also

• distance
• dynamic_measures
• find_pairs
• get_raw_alignment