AtomSets/Popup Menu - Revision history

AngelHerraez: formatting

2012-07-26T19:46:35Z

formatting

AngelHerraez: proposed changes in menu words

2010-01-23T18:12:48Z

proposed changes in menu words

AngelHerraez: filling content

2010-01-23T17:00:41Z

filling content

AngelHerraez: /* Selection of atom sets from the pop-up menu */

2010-01-23T16:43:19Z

‎Selection of atom sets from the pop-up menu

AngelHerraez: new subsection/subpage - atomo sets in pop-up menu

2010-01-23T16:19:36Z

new subsection/subpage - atomo sets in pop-up menu

New page

= Selection of atom sets from the pop-up menu =

@@ Line 1: / Line 1: @@
 = Selection of atom sets from the pop-up menu =
-Current pop-up menu (Jmol 11.9.19):
+Pop-up menu (as of Jmol 11.9.19):
 [[File:Popup_select_submenu.gif]]
 * '''Select'''
@@ Line 17: / Line 17: @@
 *** By HETATM<br />Proposed change to 'By group name'
 **** (list of hetero groups present)
-*** All PDB "HETATM" - applies script 'select hetero'<br />Proposed change to 'All hetero'
+*** All PDB "HETATM" - applies script <code>select hetero</code><br />Proposed change to 'All hetero'
-*** All solvent - applies script 'select solvent'
+*** All solvent - applies script <code>select solvent</code>
-*** All water - applies script 'select water'
+*** All water - applies script <code>select water</code>
-*** Ligand - applies script 'select ligand', which is the same as 'select hetero and not solvent'
+*** Ligand - applies script <code>select ligand</code>, which is the same as <code>select hetero and not solvent</code>
-*** Nonaqueous HETATM - applies script 'select hetero and not water'<br />Proposed change to 'Nonaqueous hetero'
+*** Nonaqueous HETATM - applies script <code>select hetero and not water</code><br />Proposed change to 'Nonaqueous hetero'
-*** Nonaqueous solvent - applies script 'select solvent and not water'
+*** Nonaqueous solvent - applies script <code>select solvent and not water</code>
 ** '''Carbohydrate''' (disabled for non-pdb files)
 *** By residue name
 **** (list of monosaccharide residues present)
-*** All - applies script 'select carbohydrate'
+*** All - applies script <code>select carbohydrate</code>
-** '''None of the above''' (disabled for non-pdb files) - applies script 'select not(hetero,protein,nucleic,carbohydrate)'
+** '''None of the above''' (disabled for non-pdb files) - applies script <code>select not(hetero,protein,nucleic,carbohydrate)</code>

@@ Line 14: / Line 14: @@
 **** (list of nucleotide residues present)
 *** (nucleic subsets)
-** '''Hetero''' (disabled for non-pdb files)
+** '''Hetero''' (disabled for non-pdb files)<br />Proposed change to other more friendly term - which one?
-*** By HETATM
+*** By HETATM<br />Proposed change to 'By group name'
 **** (list of hetero groups present)
-*** All PDB "HETATM" - applies script 'select hetero'
+*** All PDB "HETATM" - applies script 'select hetero'<br />Proposed change to 'All hetero'
 *** All solvent - applies script 'select solvent'
 *** All water - applies script 'select water'
 *** Ligand - applies script 'select ligand', which is the same as 'select hetero and not solvent'
-*** Nonaqueous HETATM - applies script 'select hetero and not water'
+*** Nonaqueous HETATM - applies script 'select hetero and not water'<br />Proposed change to 'Nonaqueous hetero'
 *** Nonaqueous solvent - applies script 'select solvent and not water'
 ** '''Carbohydrate''' (disabled for non-pdb files)

@@ Line 3: / Line 3: @@
 Current pop-up menu (Jmol 11.9.19):
 [[File:Popup_select_submenu.gif]]
-* Select
+* '''Select'''
-** Element
+** '''Element'''
-*** C
+*** (list of elements present)
-*** N
+** '''Protein''' (disabled for non-pdb files)
 *** By residue name
 *** (protein subsets)
-** Nucleic
+** '''Nucleic''' (disabled for non-pdb files)
 *** By residue name
 *** (nucleic subsets)
-** Hetero
+** '''Hetero''' (disabled for non-pdb files)
 *** By HETATM
-*** All PDB "HETATM"
+**** (list of hetero groups present)
-*** All solvent
+*** All PDB "HETATM" - applies script 'select hetero'
-*** All water
+*** All solvent - applies script 'select solvent'
-*** Ligand
+*** All water - applies script 'select water'
-*** Nonaqueous HETATM
+*** Ligand - applies script 'select ligand', which is the same as 'select hetero and not solvent'
-*** Nonaqueous solvent
+*** Nonaqueous HETATM - applies script 'select hetero and not water'
-** Carbohydrate
+*** Nonaqueous solvent - applies script 'select solvent and not water'
 *** By residue name
-*** All
+**** (list of monosaccharide residues present)
-** None of the above
+*** All - applies script 'select carbohydrate'

← Older revision		Revision as of 16:43, 23 January 2010
Line 1:		Line 1:
	= Selection of atom sets from the pop-up menu =		= Selection of atom sets from the pop-up menu =
		+
		+	Current pop-up menu (Jmol 11.9.19):
		+	[[File:Popup_select_submenu.gif]]
		+	* Select
		+	** Element
		+	*** C
		+	*** N
		+	*** O
		+	*** S
		+	** Protein
		+	*** By residue name
		+	*** (protein subsets)
		+	** Nucleic
		+	*** By residue name
		+	*** (nucleic subsets)
		+	** Hetero
		+	*** By HETATM
		+	*** All PDB "HETATM"
		+	*** All solvent
		+	*** All water
		+	*** Ligand
		+	*** Nonaqueous HETATM
		+	*** Nonaqueous solvent
		+	** Carbohydrate
		+	*** By residue name
		+	*** All
		+	** None of the above