Distance

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Revision as of 16:17, 17 April 2009 by Wayne461 (talk | contribs) (SEE ALSO)
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DESCRIPTION

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

USAGE

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

  • Get and show the distance from residue 10's alpha carbon to residue 40's alpha carbon in 1ESR:
# make the first residue 0.
zero_residues 1esr, 0
distance i. 10 and n . CA, i. 40 and n. CA
  • Get and show the distance from residue 10's alpha carbon to residue 35-42's alpha carbon in 1ESR:
# make the first residue 0.
zero_residues 1esr, 0
distance i. 10 and n . CA, i. 35-42 and n. CA
  • 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
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