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===DESCRIPTION=== | ===DESCRIPTION=== | ||
'''distance''' creates a new distance object between two selections. It will display all distances within the cutoff. | '''distance''' creates a new distance object between two selections. It will display all distances within the cutoff. | ||
| + | |||
| + | <center> | ||
| + | <gallery> | ||
| + | Image:Dist ex1.png|Example of distance. See example #1. | ||
| + | Image:Dist ex2.png|Example of distance. See example #2. | ||
| + | </gallery> | ||
| + | </center> | ||
===USAGE=== | ===USAGE=== | ||
| − | + | <source lang="python"> | |
| − | + | distance (selection1), (selection2) | |
| − | + | ||
| + | # example | ||
| + | dist i. 158 and n. CA, i. 160 and n. CA | ||
| + | </source> | ||
| − | + | 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=== | ===PYMOL API=== | ||
| Line 27: | Line 37: | ||
===EXAMPLES=== | ===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). | + | * 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"> | <source lang="python"> | ||
cmd.dist("(/mol1///1/C)","(/mol1///2/C*)") | cmd.dist("(/mol1///1/C)","(/mol1///2/C*)") | ||
| Line 33: | Line 57: | ||
or written without the PyMolScript code, | or written without the PyMolScript code, | ||
dist /mol1///1/C, /mol1///2/C* | dist /mol1///1/C, /mol1///2/C* | ||
| − | + | * Create multiple distance objects | |
| − | *Create multiple distance objects | ||
<source lang="python"> | <source lang="python"> | ||
for at1 in cmd.index("resi 10"): \ | for at1 in cmd.index("resi 10"): \ | ||
| Line 42: | Line 65: | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
| − | [[Measure_Distance]] | + | [[Measure_Distance]]<br> |
| + | [[Lines]] | ||
[[Category:Commands|distance]] | [[Category:Commands|distance]] | ||
Revision as of 20:17, 17 April 2009
DESCRIPTION
distance creates a new distance object between two selections. It will display all distances within the cutoff.
Example of distance. See example #1.
Example of distance. See example #2.
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)