Objects and Selections: Difference between revisions
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==Objects and Selections== | ==Objects and Selections== | ||
Selections are enclosed in parentheses and contain predicates, logical operations, object names, selection names and nested parenthesis: ( [... [(...) ... ]] ) | Selections are enclosed in parentheses and contain predicates, logical operations, object names, selection names and nested parenthesis: ( [... [(...) ... ]] ) | ||
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<selection> within <distance> of <selection> | <selection> within <distance> of <selection> | ||
<selection> w. <distance> of <selection> | <selection> w. <distance> of <selection> | ||
== USER COMMENTS == | |||
Working efficiently in PyMOL --- or any molecular visualization program --- requires in-depth knowledge of selections & representations. You can select objects by more than just their residue name, number, etc; for example | |||
<source lang="python"> | |||
# color blue, whatever is visible | |||
color blue, visible | |||
# show sticks, for all residues that have a b-factor of 2.0 | |||
show sticks, all and b=2.0 | |||
# show the surface representation for all residues within | |||
# 5 angstroms of any hetero atoms in all molecules | |||
show surface, byres all within 5 of het | |||
</source> | |||
Advanced selections is really where it's at, in my opinion. | |||
[[User:Inchoate|Tree]] 13:27, 11 March 2007 (CDT) | |||
Revision as of 13:27, 11 March 2007
Objects and Selections
Selections are enclosed in parentheses and contain predicates, logical operations, object names, selection names and nested parenthesis: ( [... [(...) ... ]] )
name <atom names> n. <atom names> resn <residue names> r. <residue names> resi <residue identifiers> i. <residue identifiers> chain <chain ID> c. <chain identifiers> segi <segment identifiers> s. <segment identifiers> elem <element symbol> e. <element symbols> flag <number> f. <number> alt numeric_type <numeric type> nt. <numeric type> text_type <text type> tt. <text type> b <operator> <value> q <operator> <value> formal_charge <op> <value> fc. <operator> <value> partial_charge <op> <value> pc. <operator> <value> id <original-index> hydrogen h. all * visible v. hetatm <selection> and <selection> <selection> & <selection> <selection> or <selection> <selection> | <selection> not <selection> ! <selection> byres <selection> br. <selection> byobj <selection> bo. <selection> around <distance> a. <distance> expand <distance> e. <distance> gap <distance> in <selection> like <selection> l. <selection> <selection> within <distance> of <selection> <selection> w. <distance> of <selection>
USER COMMENTS
Working efficiently in PyMOL --- or any molecular visualization program --- requires in-depth knowledge of selections & representations. You can select objects by more than just their residue name, number, etc; for example
# color blue, whatever is visible
color blue, visible
# show sticks, for all residues that have a b-factor of 2.0
show sticks, all and b=2.0
# show the surface representation for all residues within
# 5 angstroms of any hetero atoms in all molecules
show surface, byres all within 5 of het
Advanced selections is really where it's at, in my opinion.
Tree 13:27, 11 March 2007 (CDT)