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===DESCRIPTION===
 
===DESCRIPTION===
"distance" creates a new distance object between two
+
'''distance''' creates a new distance object between two selections.  It will display all distances within the cutoff.
selections.  It will display all distances within the cutoff.
 
  
 
===USAGE===
 
===USAGE===
 
  distance  
 
  distance  
 
  distance (selection1), (selection2)
 
  distance (selection1), (selection2)
 +
example: dist i. 158 and n. CA, i. 160 and n. CA
 +
 
  distance name = (selection1), (selection2) [,cutoff [,mode] ]
 
  distance name = (selection1), (selection2) [,cutoff [,mode] ]
 
   
 
   
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===PYMOL API===
 
===PYMOL API===
cmd.distance( string name, string selection1, string selection2,
+
<source lang="python">
              string cutoff, string mode )
+
cmd.distance( string name, string selection1, string selection2,
 +
              string cutoff, string mode )
 
   # returns the average distance between all atoms/frames
 
   # returns the average distance between all atoms/frames
 +
</source>
  
 
===NOTES===
 
===NOTES===
The distance wizard makes measuring distances easier than using
+
The distance wizard makes measuring distances easier than using the "dist" command for real-time operations.
the "dist" command for real-time operations.
+
 
 +
"dist" alone will show distances between selections (pk1) and (pk1), which can be set using the PkAt mouse action (usually CTRL-middle-click).
 +
 
 +
===EXAMPLES===
 +
*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.dist("(/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.dist(None, "%s`%d"%at1, "%s`%d"%at2)
 +
</source>
  
"dist" alone will show distances between selections (pk1) and (pk1),
+
===SEE ALSO===
which can be set using the PkAt mouse action (usually CTRL-middle-click).
+
[[Measure_Distance]]
  
 
[[Category:Commands|distance]]
 
[[Category:Commands|distance]]

Revision as of 16:27, 4 December 2007

DESCRIPTION

distance creates a new distance object between two selections. It will display all distances within the cutoff.

USAGE

distance 
distance (selection1), (selection2)
example: dist i. 158 and n. CA, i. 160 and n. CA 
distance name = (selection1), (selection2) [,cutoff [,mode] ]

name = name of distance object 
selection1, selection2 = atom selections
cutoff = maximum distance to display
mode = 0 (default)

PYMOL API

cmd.distance( string name, string selection1, string selection2,
              string cutoff, string mode )
   # returns the average distance between all atoms/frames

NOTES

The distance wizard makes measuring distances easier than using the "dist" command for real-time operations.

"dist" alone will show distances between selections (pk1) and (pk1), which can be set using the PkAt mouse action (usually CTRL-middle-click).

EXAMPLES

  • 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).
 cmd.dist("(/mol1///1/C)","(/mol1///2/C*)")

or written without the PyMolScript code,

dist /mol1///1/C, /mol1///2/C*
  • Create multiple distance objects
for at1 in cmd.index("resi 10"): \
   for at2 in cmd.index("resi 11"): \
       cmd.dist(None, "%s`%d"%at1, "%s`%d"%at2)

SEE ALSO

Measure_Distance