Distance - Revision history

Cchem: 1 revision

2016-04-04T00:22:29Z

1 revision

Speleo3: mode=4

2016-03-10T19:37:35Z

mode=4

Bell: 3 revisions

2015-10-19T01:04:44Z

3 revisions

Speleo3: float cutoff, int mode

2015-09-28T15:09:00Z

float cutoff, int mode

Andwar at 11:07, 13 July 2014

2014-07-13T11:07:43Z

Andwar: minor edits and referencing

2014-07-13T11:05:05Z

minor edits and referencing

Pyadmin: 18 revisions

2014-03-28T01:21:23Z

18 revisions

Speleo3: distance_exclusion

2013-01-06T08:52:45Z

distance_exclusion

Speleo3: replace deprecated syntax

2012-01-24T16:40:56Z

replace deprecated syntax

New page

'''distance''' creates a new distance object between two selections. It will display all distances within the cutoff. [[Distance]] is also used to make hydrogen bonds.

For interactive use, the '''measurement''' [[wizard]] makes measuring distances easier than using the [[distance]] command.

Calling [[distance]] without arguments will show distances between selections (pk1) and (pk1), which can be set in editing mode or using the PkAt mouse action (usually CTRL-middle-click).

<gallery align=right>
Image:Dist ex1.png|Example of distance. See example #1.
Image:Dist ex2.png|Example of distance. See example #2.
</gallery>

=Usage=
<source lang="python">
distance [ name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
</source>
'''name'''
::string: name of the distance object to create
'''selection1'''
::string: first atom selection
'''selection2'''
::string: second atom selection
'''cutoff'''
::float: longest distance to show
'''mode'''
::0: all interatomic distances
::1: only bond distances
::2: only show polar contact distances

=PYMOL API=
<source lang="python">
cmd.distance( string name, string selection1, string selection2,
string cutoff, string mode )
# returns the average distance between all atoms/frames
</source>

===EXAMPLES===
* Get and show the distance from residue 10's alpha carbon to residue 40's alpha carbon in 1ESR:
<source lang="python">
# make the first residue 0.
zero_residues 1esr, 0
distance i. 10 and n . CA, i. 40 and n. CA
</source>

* Get and show the distance from residue 10's alpha carbon to residue 35-42's alpha carbon in 1ESR:
<source lang="python">
# make the first residue 0.
zero_residues 1esr, 0
distance i. 10 and n . CA, i. 35-42 and n. CA
</source>

* This neat example shows how to create distance measurements from an atom in a molecule to all other atoms in the molecule (since PyMol supports wildcards).
<source lang="python">
cmd.distance("(/mol1///1/C)","(/mol1///2/C*)")
</source>
or written without the PyMolScript code,
dist /mol1///1/C, /mol1///2/C*
* Create multiple distance objects
<source lang="python">
for at1 in cmd.index("resi 10"): \
for at2 in cmd.index("resi 11"): \
cmd.distance(None, "%s`%d"%at1, "%s`%d"%at2)
</source>

<source lang="python">
distance (selection1), (selection2)

# example
dist i. 158 and n. CA, i. 160 and n. CA

distance mydist, 14/CA, 29/CA
distance hbonds, all, all, 3.2, mode=2
</source>

=See Also=
[[Measure_Distance]]<br>
[[Lines]]

[[Category:Commands|Distance]]

Vinnyrose at 13:45, 20 June 2009

2009-06-20T13:45:41Z

@@ Line 4: / Line 4: @@
 '''distance''' creates a new distance object between two selections.  It will display all distances within the cutoff.  [[Distance]] is also used to make hydrogen bonds.
 Calling [[distance]] without arguments will show distances between selections (pk1) and (pk1), which can be set in editing mode or using the PkAt mouse action (usually CTRL-middle-click).<br><br>
-Note: For interactive use, the '''measurement''' [[wizard]] makes measuring distances easier than using the [[distance]] command.<br>
+Note: For interactive use, the '''measurement''' [[wizard]] (from the PyMOL menu) makes measuring distances easier than using the [[distance]] command.<br>
 If you want to measure distance and avoid creating a distance object, use [[Get Distance]] or [[Distancetoatom]].<br>
+|

← Older revision		Revision as of 13:45, 20 June 2009
Line 68:		Line 68:
	[[Lines]]		[[Lines]]

−	[[Category:Commands\|~~distance~~]]	+	[[Category:Commands\|Distance]]

← Older revision	Revision as of 00:22, 4 April 2016
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@@ Line 30: / Line 30: @@
 ::2: only show polar contact distances
 ::3: like mode=0, but use [[distance_exclusion]] setting
 =PYMOL API=

← Older revision	Revision as of 01:04, 19 October 2015
(No difference)

@@ Line 34: / Line 34: @@
 <source lang="python">
 cmd.distance( string name, string selection1, string selection2,
-               string cutoff, string mode )
+               float cutoff, int mode )
     # returns the average distance between all atoms/frames
 </source>

@@ Line 1: / Line 1: @@
 '''distance''' creates a new distance object between two selections.  It will display all distances within the cutoff.  [[Distance]] is also used to make hydrogen bonds.
+Calling [[distance]] without arguments will show distances between selections (pk1) and (pk1), which can be set in editing mode or using the PkAt mouse action (usually CTRL-middle-click).<br><br>
-For interactive use, the '''measurement''' [[wizard]] makes measuring distances easier than using the [[distance]] command.
+Note: For interactive use, the '''measurement''' [[wizard]] makes measuring distances easier than using the [[distance]] command.<br>
+If you want to measure distance and avoid creating a distance object, use [[Get Distance]] or [[Distancetoatom]].<br>
 Calling [[distance]] without arguments will show distances between selections (pk1) and (pk1), which can be set in editing mode or using the PkAt mouse action (usually CTRL-middle-click).
+[[Image:Dist ex1.png|300px|Example of distance.  See example #1.]]
-<gallery align=right>
-Image:Dist ex1.png|Example of distance.  See example #1.
+[[Image:Dist ex2.png|300px|Example of distance.  See example #2.]]
-Image:Dist ex2.png|Example of distance.  See example #2.
+||
-</gallery>
+|}
 =Usage=
@@ Line 74: / Line 77: @@
 =See Also=
-[[Measure_Distance]]<br>
+* [[Get Distance]] # Avoid creating an object
-[[Lines]]
+* [[Distancetoatom]] # Automated script for distances to a point
 [[Category:Commands|Distance]]

← Older revision	Revision as of 01:21, 28 March 2014
(No difference)