Bell: 3 revisions

2014-11-26T15:24:25Z

3 revisions

Sbliven: Fixing capitalization

2014-11-24T09:24:14Z

Fixing capitalization

Andwar: typos

2014-07-13T11:09:01Z

typos

Andwar: created page for distancetoatoms

2014-07-13T10:42:55Z

created page for distancetoatoms

New page

{{Infobox script-repo
|type = Python Module
|filename = distancetoatom.py
|author = [[User:Andwar|Andreas Warnecke]] and [[User:Jaredsampson|Jared Sampson]]
|license = BSD-2-Clause
}}
[[Image:distancetoatom_0.png|right|300px|get distance to atoms within cutoff]]

==About distancetoatom==
'''distancetoatom''' prints all distanced 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==
{|-
||
<source lang="python">
distancetoatom [ origin [, cutoff [, filename [, selection [, state [, property_name [, coordinates [, decimals [, sort [, quiet ]]]]]]]]]]
</source>
||
|}

===Arguments===
{| class="wikitable"
!colspan="3;"|Arguments for distancetoatom
|- style="text-align:center;"
! scope="col"| Keyword
! scope="col"| Default
! scope="col"| What it does
|-
! scope="row"| origin
| style="text-align:center;"| pk1
| "origin" defines the coordinates for the origin and can be:
1. a list with coordinates [x,y,z] 
2. a single atom selection string 
3. a multi-atom selection string (center will be used)
|-
! scope="row"| cutoff
| style="text-align:center;"| 10
| "cutoff" defines the maximum distance, atoms further away are not considered
|-
! scope="row"| filename
| style="text-align:center;"| 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. 
(omit or set to "", None, 0 or False to disable)
|-
! scope="row"| selection
| style="text-align:center;"| all
| only atoms within "selection" (and cutoff distance) will be used for calculation
|-
! scope="row"| state
| style="text-align:center;"| 0
| "state" is the state that will be used for calculations
use 0 (omit), to automatically use the current state
|-
! scope="row"| property_name
| style="text-align:center;"| 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) 
NB! older PyMOL versions only support b or q and the distance will overwrite this property if set.
|-
! scope="row"| coordinates
| style="text-align:center;"| 0
| "coordinates" toggles whether, besides distance, the atom coordinates will be included in the report.
|-
! scope="row"| decimals
| style="text-align:center;"| 3
| "decimals" is the number of decimal places calculated.
Note that PDB files do not support a higher resolution than 3.
|-
! scope="row"| sort
| style="text-align:center;"| 1
| "sort" defines how the output will be sorted:
1: ascending (default) 
0: no sorting (by selection) 
-1: descending
|-
! scope="row"| quiet
| style="text-align:center;"| 1
| toggle verbosity
|}

==Examples==
{|-
||
<source lang="python">
# 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
</source>
||
[[Image:distancetoatom_2.png|300px|Example 2]] 
[[Image:distancetoatom_1.png|300px|Example 3]]
|}

==SEE ALSO==
* [[Distance]]
* [[Get Distance]]
* [[Get raw distances]]

[[Category:Script_Library]]
[[Category:UI_Scripts]]
[[Category:Math_Scripts]]
[[Category:Biochemical_Properties]]
[[Category:Biochemical_Scripts]]

← Older revision	Revision as of 15:24, 26 November 2014
(No difference)

@@ Line 10: / Line 10: @@
 '''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.<br>
 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]]
+* For instruction on setting up plugin import see [[Git intro]] or [[Plugin Manager]]
 ==Usage==

Distancetoatom - Revision history

Bell: 3 revisions

Sbliven: Fixing capitalization

Andwar: typos

Andwar: created page for distancetoatoms