Selecting - Revision history

AngelHerraez: correct misguiding phrases: "display" doe snot select atoms

2009-06-27T22:08:45Z

correct misguiding phrases: "display" doe snot select atoms

AngelHerraez at 16:00, 22 September 2007

2007-09-22T16:00:13Z

AngelHerraez: /* Select (A or B ) and (not (A and B)) */

2007-09-22T15:57:21Z

‎Select (A or B ) and (not (A and B))

AngelHerraez: /* Combining selection statements */

2007-09-22T15:56:12Z

‎Combining selection statements

Pimpim: /* Geometric expressions */

2007-09-12T17:44:58Z

‎Geometric expressions

Pimpim: /* Geometric expressions */

2007-09-12T17:09:30Z

‎Geometric expressions

Pimpim: /* Atom expressions */

2007-09-12T16:49:15Z

‎Atom expressions

Pimpim: /* Atom expressions */

2007-09-12T16:47:36Z

‎Atom expressions

AngelHerraez: correction of syntax: AND needed before NOT

2007-07-02T18:47:38Z

correction of syntax: AND needed before NOT

Pimpim at 08:13, 28 June 2007

2007-06-28T08:13:54Z

@@ Line 9: / Line 9: @@
 * '''display *.CA''' displays all C-alpha atoms.
-* '''select _C''' selects all carbon atoms, equivalent to '''select *.C??'''
+* '''select _C''' selects all carbon atoms, usually (but not necessarily) equivalent to '''select *.C??''' (the first identifies the element, the second just the atomm names and is only good for pdb files)
-* '''select [ALA]''' selects all atoms in ALA amino acids.
+* '''select [ALA]''' selects all atoms in alanine residues (pdb file format)
-* '''display 1''', this will select the first amino acid residue and/or molecule. If a file contains various molecules, and they are all numbered starting from 1, this will select all first molecules or first residues of peptide strings.
+* '''display 1''', this will display only the first amino acid residue and/or molecule. If a file contains various molecules, and they are all numbered starting from 1, this will display only all first molecules or first residues of peptide strings.
-* '''display 1:A''', if multiple chains are present, this will select residue 1 of chain A.
+* '''display 1:A''', if multiple chains are present, this will display only atoms in residue 1 of chain A.
 = Geometric expressions =
@@ Line 18: / Line 18: @@
 Of course one can select based on distances:
-* '''display within(3.0,hydrophobic)''' Selects all atoms of hydrophobic residues, and all atoms within 3.0 Angstroms from these residues.
+* '''display within(3.0,hydrophobic)''' displays only all atoms of hydrophobic residues (pdb file format), and all atoms within 3.0 Angstroms from these residues.
 It is for the newest versions of Jmol also possible to select atoms according to [http://chemapps.stolaf.edu/jmol/docs/?#planeexpressions plane selections].
-One can select atoms within 0.01 angstrom distance within a plane (and by combing two of these selections, on a line). To display atoms up to 6 Angstrom away from a surface with miller index 1 1 1, use:
+One can select atoms within 0.01 angstrom distance within a plane (and by combining two of these selections, on a line). To display atoms up to 6 Angstrom away from a surface with Miller index 1 1 1, use:
 * '''display within (-6, hkl, {1 1 1})'''

@@ Line 2: / Line 2: @@
 Selecting can be done via atom expressions or based on topology or geometry.
-The selection expressions used in Jmol can be used for the "select" and the "display within" commands.
+Atom expressions in Jmol can be used in "select", "display", "hide" commands, as well as many others.
 = Atom expressions =

@@ Line 71: / Line 71: @@
 [[Image:Select_A_not_B.jpg]] Selects the atoms in the peptide chain, except those that are oxygen atoms.
-=== Select (A or B ) and (not (A and B)) ===
+=== Select (A or B ) and not (A and B) ===
 [[Image:Select_A_or_B_and_not_A_and_B.jpg]] Selects all the peptide chain atoms and all the oxygen atoms, but not the oxygen atoms in the peptide chain.

@@ Line 62: / Line 62: @@
 === Select A or B ===
 [[Image:Select_A_or_B.jpg]] Selects all atoms in the peptide chain, and all oxygen atoms, including the oxygen atoms in the water molecules.
@@ Line 68: / Line 69: @@
 === Select A and not B ===
-[[Image:Select_A_not_B.jpg]] Selects the atoms in the peptide chain, but not the ones that are oxygen atoms.
+[[Image:Select_A_not_B.jpg]] Selects the atoms in the peptide chain, except those that are oxygen atoms.
 === Select (A or B ) and (not (A and B)) ===
 [[Image:Select_A_or_B_and_not_A_and_B.jpg]] Selects all the peptide chain atoms and all the oxygen atoms, but not the oxygen atoms in the peptide chain.

@@ Line 16: / Line 16: @@
 = Geometric expressions =
-Of course one can select based on distances.
+Of course one can select based on distances:
 * '''display within(3.0,hydrophobic)''' Selects all atoms of hydrophobic residues, and all atoms within 3.0 Angstroms from these residues.
 It is for the newest versions of Jmol also possible to select atoms according to [http://chemapps.stolaf.edu/jmol/docs/?#planeexpressions plane selections].
-One can select atoms within 0.01 angstrom distance within a plane (and by combing two of these selections, on a line).
+One can select atoms within 0.01 angstrom distance within a plane (and by combing two of these selections, on a line). To display atoms up to 6 Angstrom away from a surface with miller index 1 1 1, use:
-* ''' '''
+* '''display within (-6, hkl, {1 1 1})'''
 = Topology expressions =

← Older revision		Revision as of 17:09, 12 September 2007
Line 16:		Line 16:
	= Geometric expressions =		= Geometric expressions =

		+	Of course one can select based on distances.
		+
		+	* '''display within(3.0,hydrophobic)''' Selects all atoms of hydrophobic residues, and all atoms within 3.0 Angstroms from these residues.
		+
		+	It is for the newest versions of Jmol also possible to select atoms according to [http://chemapps.stolaf.edu/jmol/docs/?#planeexpressions plane selections].
		+
		+	One can select atoms within 0.01 angstrom distance within a plane (and by combing two of these selections, on a line).
		+
		+	* ''' '''

	= Topology expressions =		= Topology expressions =

@@ Line 8: / Line 8: @@
 Common examples:
-* [b]display *.CA[/b] displays all C-alpha atoms.
+* '''display *.CA''' displays all C-alpha atoms.
-* [b]select _C[/b] selects all carbon atoms, equivalent to [b]select *.C??[/b]
+* '''select _C''' selects all carbon atoms, equivalent to '''select *.C??'''
-* [b]select [ALA][/b] selects all atoms in ALA amino acids.
+* '''select [ALA]''' selects all atoms in ALA amino acids.
-* [b]display 1[/b], this will select the first amino acid residue and/or molecule. If a file contains various molecules, and they are all numbered starting from 1, this will select all first molecules or first residues of peptide strings.
+* '''display 1''', this will select the first amino acid residue and/or molecule. If a file contains various molecules, and they are all numbered starting from 1, this will select all first molecules or first residues of peptide strings.
-* [b]display 1:A[/b], if multiple chains are present, this will select residue 1 of chain A.
+* '''display 1:A''', if multiple chains are present, this will select residue 1 of chain A.
 = Geometric expressions =