Distance

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