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Difference between revisions of "Distance"
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===DESCRIPTION=== | ===DESCRIPTION=== | ||
| − | + | '''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] ] | ||
| Line 14: | Line 15: | ||
===PYMOL API=== | ===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 | # 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> | ||
| − | + | ===SEE ALSO=== | |
| − | + | [[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)