Distancetoatom
| Type | Python Module |
|---|---|
| Download | distancetoatom.py |
| Author(s) | Andreas Warnecke and Jared Sampson |
| License | BSD-2-Clause |
| This code has been put under version control in the project Pymol-script-repo | |
About distancetoatom
distancetoatom prints all distances between a specified atom, coordinate or group selection center and all atoms within cutoff distance that are part of the selection.
All coordinates and distances can be saved in a csv-style text file report and/or can be stored in a (custom) atom property, if defined.
- For instruction on setting up plugin import see Git intro or Plugin Manager
Usage
distancetoatom [ origin [, cutoff [, filename [, selection [, state [, property_name [, coordinates [, decimals [, sort [, quiet ]]]]]]]]]]
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Arguments
| Arguments for distancetoatom | ||
|---|---|---|
| Keyword | Default | What it does |
| origin | pk1 | "origin" defines the coordinates for the origin and can be:
1. a list with coordinates [x,y,z] |
| cutoff | 10 | "cutoff" defines the maximum distance, atoms further away are not considered |
| filename | None | "filename" is the name of a report file that will be created (optional).
set to e.g. 'report.txt' to create a report. This file is CSV style and can be imported into EXCEL. |
| selection | all | only atoms within "selection" (and cutoff distance) will be used for calculation |
| state | 0 | "state" is the state that will be used for calculations
use 0 (omit), to automatically use the current state |
| property_name | p.dist | "property_name" defines a (custom) property in which the calculated distance will be stored.
This can be used e.g. for labeling or spectrum coloring etc. (cf. examples) |
| coordinates | 0 | "coordinates" toggles whether, besides distance, the atom coordinates will be included in the report. |
| decimals | 3 | "decimals" is the number of decimal places calculated.
Note that PDB files do not support a higher resolution than 3. |
| sort | 1 | "sort" defines how the output will be sorted:
1: ascending (default) |
| quiet | 1 | toggle verbosity |
Examples
# make function available to PyMOL
import distancetoatom
##############################
# Example 1: print all distances
frag LYS
edit name CA
distancetoatom
##############################
# Example 2: print all distances to file
fetch 1cll, async=0
distancetoatom origin=/1cll//A/CA`150/CA, filename=distances.txt, selection=elem O, property_name=b
# the file is CSV-format and can be imported, e.g. to EXCEL
# format
hide everything
select byres (resi 150 expand 5 and not resn hoh)
show_as sticks, sele
util.cbaw sele
show_as spheres, resi 150
zoom sele
##########
# Label by stored distance (property_name)
label sele and elem O, "%.2f"%b
##############################
# Example 3: color an object by distance to a coordinate
fetch 1cll, async=0
distancetoatom [0,0,0], cutoff=1000, property_name=b
# the distance is stored in the b-factor in this case
# newer PyMOL versions support custom properties, e.g. "p.dist"
spectrum b, rainbow_rev
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